WorldWideScience

Sample records for two-letter aperiodic sequences

  1. Critical behavior of marginal aperiodic sequences: a Monte Carlo study

    Science.gov (United States)

    Branco, Nilton

    2007-03-01

    We study layered marginal aperiodic sequences for the Ising and q=8 Potts model on a square lattice. The phase transition is continuous for the former and first-order for the latter. Using the Wolff algorithm we calculate critical exponents and the critical temperature for the Potts model when the interaction constant can assume two values, according to an aperiodic sequence: the period-doubling one for the Ising model and the Fibonacci one for the Potts model. These sequences and models chracterize marginal critical behavior, according to the Luck criterion and, therefore, interaction-dependent exponents are expected for a continuous transition. For first-order phase transitions, no study so far has been done on the influence of marginal sequences.

  2. Focusing properties of diffractive lenses constructed with the aperiodic m-bonacci sequence

    Science.gov (United States)

    Furlan, Walter D.; Ferrando, Vicente; Monsoriu, Juan A.

    2015-01-01

    In this contribution we present a new family of diffractive lenses which are designed using the m-bonacci sequence. These lenses are a generalization of the Fibonacci Zone Plates previously reported. Diffractive elements of this type are called aperiodic zone plates because they are characterized by a radial profile that follows a given deterministic aperiodic sequence (Cantor set, Thue-Morse, Fibonacci...). Aperiodic lenses have demonstrated new interesting focusing and imaging properties that have found applications in different fields such as soft X-ray microscopy and spectral domain optical coherence tomography. Here, we show that m-bonacci zone plates are inherently bifocal lenses. We demonstrate that the relative separation of their foci depends on the m-value of the sequence and also can be correlated with the generalized golden ratio. As a particular case, the properties of the m-bonacci sequence with m=2 and m=3, called Fibonacci and Tribonacci Zone Plates respectively are discussed.

  3. Aperiodic quantum XXZ chains: Renormalization-group results

    Science.gov (United States)

    Vieira, André P.

    2005-04-01

    We report a comprehensive investigation of the low-energy properties of antiferromagnetic quantum XXZ spin chains with aperiodic couplings. We use an adaptation of the Ma-Dasgupta-Hu renormalization-group method to obtain analytical and numerical results for the low-temperature thermodynamics and the ground-state correlations of chains with couplings following several two-letter aperiodic sequences, including the quasiperiodic Fibonacci and other precious-mean sequences, as well as sequences inducing strong geometrical fluctuations. For a given aperiodic sequence, we argue that in the easy-plane anisotropy regime, intermediate between the XX and Heisenberg limits, the general scaling form of the thermodynamic properties is essentially given by the exactly known XX behavior, providing a classification of the effects of aperiodicity on XXZ chains. We also discuss the nature of the ground-state structures and their comparison with the random-singlet phase characteristic of random-bond chains.

  4. Iteration of Differentiable Functions under m-Modal Maps with Aperiodic Kneading Sequences

    Directory of Open Access Journals (Sweden)

    Maria F. Correia

    2012-01-01

    Full Text Available We consider the dynamical system (, , where is a class of differentiable functions defined on some interval and : → is the operator ∶=∘, where is a differentiable m-modal map. Using an algorithm, we obtained some numerical and symbolic results related to the frequencies of occurrence of critical values of the iterated functions when the kneading sequences of are aperiodic. Moreover, we analyze the evolution as well as the distribution of the aperiodic critical values of the iterated functions.

  5. New theoretical bounds on the aperiodic correlation functions of binary sequences

    Institute of Scientific and Technical Information of China (English)

    PENG Daiyuan; FAN Pingzhi

    2005-01-01

    In order to reduce or eliminate the multiple access interference in code division multiple access (CDMA) systems, we need to design a set of spreading sequences with good autocorrelation functions (ACF) and crosscorrelation functions (CCF). The importance of the spreading codes to CDMA systems cannot be overemphasized, for the type of the code used, its length, and its chip rate set bounds on the capability of the system that can be changed only by changing the code. Several new lower bounds which are stronger than the well-known Sarwate bounds, Welch bounds and Levenshtein bounds for binary sequence set with respect to the spreading sequence length, family size, maximum aperiodic autocorrelation sidelobe and maximum aperiodic crosscorrelation value are established.

  6. Optical properties of structures composed of periodic, quasi-periodic, and aperiodic sequences of particulate monolayers

    Science.gov (United States)

    Loiko, V. A.; Miskevich, A. A.

    2017-01-01

    The spectra of the coherent transmission and reflection coefficients of multilayers consisting of the periodic, Fibonacci (quasi-periodic), and Thue-Morse (aperiodic) sequences of plane-parallel monolayers of monodisperse spherical alumina and silica particles are investigated using the quasi-crystalline approximation (QCA) and the transfer matrix method (TMM). The additional opportunities for the transmission and reflection spectra manipulation in comparison with the periodic sequence of monolayers are demonstrated. Photonic band gaps in the spectra of the particulate structures are shifted to the short-wavelength range in comparison with those for systems of homogeneous layers. The shift is larger for the Thue-Morse sequence. The widths of the photonic band gaps for particulate systems are narrower than the ones for multilayers consisting of homogeneous layers of an equivalent volume of matter. The results can be used to create optical, optoelectronics, and photonics devices—for example, multispectral filters, light emitting diodes, solar cells, displays.

  7. Aperiodic Quantum Random Walks

    CERN Document Server

    Ribeiro, P; Mosseri, R; Ribeiro, Pedro; Milman, Perola; Mosseri, Remy

    2004-01-01

    We generalize the quantum random walk protocol for a particle in a one-dimensional chain, by using several types of biased quantum coins, arranged in aperiodic sequences, in a manner that leads to a rich variety of possible wave function evolutions. Quasiperiodic sequences, following the Fibonacci prescription, are of particular interest, leading to a sub-ballistic wavefunction spreading. In contrast, random sequences leads to diffusive spreading, similar to the classical random walk behaviour. We also describe how to experimentally implement these aperiodic sequences.

  8. Effect of Aperiodicity on the Charge Transfer Through DNA Molecules

    Science.gov (United States)

    Ghosh, Angsula; Chaudhuri, Puspitapallab

    The effect of aperiodicity on the charge transfer process through DNA molecules is investigated using a tight-binding model. Single-stranded aperiodic Fibonacci polyGC and polyAT sequences along with aperiodic Rudin-Shapiro poly(GCAT) sequences are used in the study. Based on the tight-binding model, molecular orbital calculations of the DNA chains are performed and ionization potentials compared, as this might be relevant to understanding the charge transfer process. Charges migrate through the sequences in a multistep hopping process. Results for current conduction through aperiodic sequences are compared with those for the corresponding periodic sequences. We find that dinucleotide aperiodic Fibonacci sequences decrease the current while tetranucleotide aperiodic Rudin-Shapiro sequences increase the current when compared with the corresponding periodic sequences. The conductance in all cases decays exponentially as the sequence length increases.

  9. Functional continuity: did field-induced oriented aperiodic constraints at Life's origin aid its sequence-based evolution?

    Science.gov (United States)

    Mitra-Delmotte, G.; Mitra, A. N.

    2014-04-01

    A non-biological analog undergoing Darwinian-like evolution could have enhanced the probability of many crucial independent bottom-up emergent steps, engendered within its premises, and smoothen the inanimate-animate transition. Now, the higher-level environment-mutable DNA sequences influence the lower-level pattern of oriented templates (enzymes, lipid membranes, RNA) in the organized cell matrix and hence their associated substrate-dynamics; note how templates are akin to local fields, kinetically constraining reactant orientations. Since the lowerlevel is likely the more primitive of the two (rather than Cairns-Smith's "readily available" rigid clay crystal sequence-based replicators as a memory-like basis for slowly mutating predecessor-patterns enroute to complex RNA-based Darwinian evolution), a gradual thermodynamic-to-kinetic transition in an isotropic medium, is proposed as driven by some order-parameter --via "available" field-responsive dipolar colloid networks, as apart from bio-organics, mineral colloids also can display liquid crystal (LC) phases (see [1]). An access to solid-like orientational order in a fluid matrix suggests how aperiodic patterns can be influenced and sustained (a la homeostasis) via external inhomogeneous fields (e.g. magnetic rocks); this renders these cooperative networks with potential as confining host-media, whose environment-sensitivity can not only influence their sterically-coupled guest-substrates but also their network properties (the latter can enable 'functions' like spontaneous transport under non-equilibrium suggesting a natural basis for their selection by the environment). In turn LC systems could have been preceded by even simpler anisotropic fluid hosts, viz., external field-induced mineral magnetic nanoparticle (MNP) aggregates. Indeed, the capacity of an MNP to couple its magnetic and rotational d.o.f.s suggests how an environment-sensitive field-influenced network of interacting dipolar colloids close to

  10. Stochastic Flips on Two-letter Words

    CERN Document Server

    Bodini, Olivier; Regnault, Damien

    2010-01-01

    This paper introduces a simple Markov process inspired by the problem of quasicrystal growth. It acts over two-letter words by randomly performing \\emph{flips}, a local transformation which exchanges two consecutive different letters. More precisely, only the flips which do not increase the number of pairs of consecutive identical letters are allowed. Fixed-points of such a process thus perfectly alternate different letters. We show that the expected number of flips to converge towards a fixed-point is bounded by $O(n^3)$ in the worst-case and by $O(n^{5/2}\\ln{n})$ in the average-case, where $n$ denotes the length of the initial word.

  11. Mathematics of aperiodic order

    CERN Document Server

    Lenz, Daniel; Savinien, Jean

    2015-01-01

    What is order that is not based on simple repetition, that is, periodicity? How must atoms be arranged in a material so that it diffracts like a quasicrystal? How can we describe aperiodically ordered systems mathematically? Originally triggered by the – later Nobel prize-winning – discovery of quasicrystals, the investigation of aperiodic order has since become a well-established and rapidly evolving field of mathematical research with close ties to a surprising variety of branches of mathematics and physics. This book offers an overview of the state of the art in the field of aperiodic order, presented in carefully selected authoritative surveys. It is intended for non-experts with a general background in mathematics, theoretical physics or computer science, and offers a highly accessible source of first-hand information for all those interested in this rich and exciting field. Topics covered include the mathematical theory of diffraction, the dynamical systems of tilings or Delone sets, their cohomolog...

  12. Cyclotomic Aperiodic Substitution Tilings

    Directory of Open Access Journals (Sweden)

    Stefan Pautze

    2017-01-01

    Full Text Available The class of Cyclotomic Aperiodic Substitution Tilings (CASTs is introduced. Its vertices are supported on the 2 n -th cyclotomic field. It covers a wide range of known aperiodic substitution tilings of the plane with finite rotations. Substitution matrices and minimal inflation multipliers of CASTs are discussed as well as practical use cases to identify specimen with individual dihedral symmetry D n or D 2 n , i.e., the tiling contains an infinite number of patches of any size with dihedral symmetry D n or D 2 n only by iteration of substitution rules on a single tile.

  13. Aperiodic Volume Optics

    Science.gov (United States)

    Gerke, Tim D.

    Presented in this thesis is an investigation into aperiodic volume optical devices. The three main topics of research and discussion are the aperiodic volume optical devices that we call computer-generated volume holograms (CGVH), defects within periodic 3D photonic crystals, and non-periodic, but ordered 3D quasicrystals. The first of these devices, CGVHs, are designed and investigated numerically and experimentally. We study the performance of multi-layered amplitude computer-generated volume holograms in terms of efficiency and angular/frequency selectivity. Simulation results show that such aperiodic devices can increase diffraction efficiency relative to periodic amplitude volume holograms while maintaining angular and wavelength selectivity. CGVHs are also designed as voxelated volumes using a new projection optimization algorithm. They are investigated using a volumetric diffraction simulation and a standard 3D beam propagation technique as well as experimentally. Both simulation and experiment verify that the structures function according to their design. These represent the first diffractive structures that have the capacity for generating arbitrary transmission and reflection wave fronts and that provide the ability for multiplexing arbitrary functionality given different illumination conditions. Also investigated and discussed in this thesis are 3D photonic crystals and quasicrystals. We demonstrate that these devices can be fabricated using a femtosecond laser direct writing system that is particularly appropriate for fabrication of such arbitrary 3D structures. We also show that these devices can provide 3D partial bandgaps which could become complete bandgaps if fabricated using high index materials or by coating lower index materials with high index metals. Our fabrication method is particularly suited to the fabrication of engineered defects within the periodic or quasi-periodic systems. We demonstrate the potential for fabricating defects within

  14. Fixed Point and Aperiodic Tilings

    CERN Document Server

    Durand, Bruno; Shen, Alexander

    2008-01-01

    An aperiodic tile set was first constructed by R.Berger while proving the undecidability of the domino problem. It turned out that aperiodic tile sets appear in many topics ranging from logic (the Entscheidungsproblem) to physics (quasicrystals) We present a new construction of an aperiodic tile set that is based on Kleene's fixed-point construction instead of geometric arguments. This construction is similar to J. von Neumann self-reproducing automata; similar ideas were also used by P. Gacs in the context of error-correcting computations. The flexibility of this construction allows us to construct a ``robust'' aperiodic tile set that does not have periodic (or close to periodic) tilings even if we allow some (sparse enough) tiling errors. This property was not known for any of the existing aperiodic tile sets.

  15. A Finite Abelian Group of Two-Letter Inversions

    Directory of Open Access Journals (Sweden)

    Sherwin E. Balbuena

    2015-11-01

    Full Text Available In abstract algebra, the study of concrete groups is fundamentally important to beginners. Most commonly used groups as examples are integer addition modulo n, real number addition and multiplication, permutation groups, and groups of symmetry. The last two examples are finite non-abelian groups and can be investigated with the aid of concrete representations. This study presents a finite abelian group of inversions of two letter symbols with vertical and horizontal axes of symmetry and whose binary operation is established through motions like alternation, rotation, reflection, and a combination of two or all motions.

  16. When Periodicities Enforce Aperiodicity

    Science.gov (United States)

    Bédaride, Nicolas; Fernique, Thomas

    2015-05-01

    Non-periodic tilings and local rules are commonly used to model the long range aperiodic order of quasicrystals and the finite-range energetic interactions that stabilize them. This paper focuses on planar rhombus tilings, which are tilings of the Euclidean plane, which can be seen as an approximation of a real plane embedded in a higher dimensional space. Our main result is a characterization of the existence of local rules for such tilings when the embedding space is four-dimensional. The proof is an interplay of algebra and geometry that makes use of the rational dependencies between the coordinates of the embedded plane. We also apply this result to some cases in a higher dimensional embedding space, notably tilings with n-fold rotational symmetry.

  17. Renormalization of aperiodic model lattices: spectral properties

    CERN Document Server

    Kroon, L

    2003-01-01

    Many of the published results for one-dimensional deterministic aperiodic systems treat rather simplified electron models with either a constant site energy or a constant hopping integral. Here we present some rigorous results for more realistic mixed tight-binding systems with both the site energies and the hopping integrals having an aperiodic spatial variation. It is shown that the mixed Thue-Morse, period-doubling and Rudin-Shapiro lattices can be transformed to on-site models on renormalized lattices maintaining the individual order between the site energies. The character of the energy spectra for these mixed models is therefore the same as for the corresponding on-site models. Furthermore, since the study of electrons on a lattice governed by the Schroedinger tight-binding equation maps onto the study of elastic vibrations on a harmonic chain, we have proved that the vibrational spectra of aperiodic harmonic chains with distributions of masses determined by the Thue-Morse sequence and the period-doubli...

  18. Band structures and localization properties of aperiodic layered phononic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Yan Zhizhong, E-mail: zzyan@bit.edu.cn [Department of Applied Mathematics, Beijing Institute of Technology, Beijing 100081 (China); Zhang Chuanzeng [Department of Civil Engineering, University of Siegen, D-57078 Siegen (Germany)

    2012-03-15

    The band structures and localization properties of in-plane elastic waves with coupling of longitudinal and transverse modes oblique propagating in aperiodic phononic crystals based on Thue-Morse and Rudin-Shapiro sequences are studied. Using transfer matrix method, the concept of the localization factor is introduced and the correctness is testified through the Rytov dispersion relation. For comparison, the perfect periodic structure and the quasi-periodic Fibonacci system are also considered. In addition, the influences of the random disorder, local resonance, translational and/or mirror symmetries on the band structures of the aperiodic phononic crystals are analyzed in this paper.

  19. Band structures and localization properties of aperiodic layered phononic crystals

    Science.gov (United States)

    Yan, Zhi-Zhong; Zhang, Chuanzeng

    2012-03-01

    The band structures and localization properties of in-plane elastic waves with coupling of longitudinal and transverse modes oblique propagating in aperiodic phononic crystals based on Thue-Morse and Rudin-Shapiro sequences are studied. Using transfer matrix method, the concept of the localization factor is introduced and the correctness is testified through the Rytov dispersion relation. For comparison, the perfect periodic structure and the quasi-periodic Fibonacci system are also considered. In addition, the influences of the random disorder, local resonance, translational and/or mirror symmetries on the band structures of the aperiodic phononic crystals are analyzed in this paper.

  20. Lasing in an optimized deterministic aperiodic nanobeam cavity

    Science.gov (United States)

    Moon, Seul-Ki; Jeong, Kwang-Yong; Noh, Heeso; Yang, Jin-Kyu

    2016-12-01

    We have demonstrated lasing action from partially extended modes in deterministic aperiodic nanobeam cavities inflated by Rudin-Shapiro sequence with two different air holes at room temperature. By varying the size ratio of the holes and hence the structural aperiodicity, different optical lasing modes were obtained with maximized quality factors. The lasing characteristics of the partially extended modes were confirmed by numerical simulations based on scanning microscope images of the fabricated samples. We believe that this partially extended nanobeam modes will be useful for label-free optical biosensors.

  1. Analytical and numerical studies of disordered spin-1 Heisenberg chains with aperiodic couplings

    OpenAIRE

    Grande, H. L. Casa; Laflorencie, N.; Alet, F.; Vieira, A. P.

    2013-01-01

    We investigate the low-temperature properties of the one-dimensional spin-1 Heisenberg model with geometric fluctuations induced by aperiodic but deterministic coupling distributions, involving two parameters. We focus on two aperiodic sequences, the Fibonacci sequence and the 6-3 sequence. Our goal is to understand how these geometric fluctuations modify the physics of the (gapped) Haldane phase, which corresponds to the ground state of the uniform spin-1 chain. We make use of different adap...

  2. Scale dependent partitioning of one-dimensional aperiodic set diffraction

    Science.gov (United States)

    Elkharrat, A.

    2004-06-01

    We give a multiresolution partition of pure point parts of diffraction patterns of one-dimensional aperiodic sets. When an aperiodic set is related to the Golden Ratio, denoted by tau, it is well known that the pure point part of its diffractive measure is supported by the extension ring of tau, denoted by mathbb{Z}[tau]. The partition we give is based on the formalism of the so called tau-integers, denoted by mathbb{Z}_tau. The set of tau-integers is a selfsimilar set obeying mathbb{Z}_tau/tau^{j-1}subsetmathbb{Z}_tau/tau^j subset mathbb{Z}_tau/tau^{j + 1} subsetmathbb{Z}[tau], jinmathbb{Z}. The pure point spectrum is then partitioned with respect to this “Russian doll” like sequence of subsets mathbb{Z}_tau/tau^j. Thus we deduce the partition of the pure point part of the diffractive measure of aperiodic sets.

  3. Aperiodic order and spectral properties

    OpenAIRE

    Baake, Michael; Damanik, David; Grimm, Uwe

    2015-01-01

    This article presents a very gentle introduction to the field of aperiodic order, aimed at a general audience. It is intended to provide a "Snapshot of Modern Mathematics" relating to the Oberwolfach mini-workshop "Dynamical versus Diffraction Spectra in the Theory of Quasicrystals" in November/December 2014.

  4. PREFACE: 6th International Conference on Aperiodic Crystals (APERIODIC'09)

    Science.gov (United States)

    Grimm, Uwe; McGrath, Rónán; Degtyareva, Olga; Sharma, Hem Raj

    2010-04-01

    Aperiodic Logo Aperiodic'09, the sixth International Conference on Aperiodic Crystals, took place in Liverpool 13-18 September 2009. It was the first major conference in this interdisciplinary research field held in the UK. The conference, which was organised under the auspices of the Commission on Aperiodic Crystals of the International Union of Crystallography (IUCr), followed on from Aperiodic'94 (Les Diablerets, Switzerland), Aperiodic'97 (Alpe d'Huez, France), Aperiodic'2000 (Nijmegen, The Netherlands), Aperiodic'03 (Belo Horizonte, Brazil) and Aperiodic'06 (Zao, Japan). The next conference in the series will take place in Australia in 2012. The Aperiodic conference series is itself the successor to a series of Conferences on Modulated Structures, Polytypes and Quasicrystals (MOSPOQ), which were held in Marseilles (France) in 1984, Wroclaw (Poland) in 1986, Varanasi (India) in 1988 and Balatonszeplak (Hungary) in 1991. The remit of the conference covers two broad areas of research on aperiodic crystals, incommensurately modulated and composite crystals on the one hand, and quasicrystals on the other hand, sharing the property that they are aperiodically ordered solids. In addition, the conference also featured recent research on complex metal alloys, which are in fact periodically ordered solids. However, the term complex refers to their large unit cells, which may contain thousands of atoms, and as a consequence complex metal alloys share some of the properties of quasicrystalline solids. Aperiodic'09 attracted about 110 participants from across the world, including 20 UK-based scientists (the second largest group after Japan who sent 21 delegates). A particular feature of the conference series is its interdisciplinary character, and once again the range of disciplines of participants included mathematics, physics, crystallography and materials science. The programme started with three tutorial lectures on Sunday afternoon, presenting introductory overviews

  5. Optical gaps, mode patterns and dipole radiation in two-dimensional aperiodic photonic structures

    Science.gov (United States)

    Boriskina, Svetlana V.; Gopinath, Ashwin; Negro, Luca Dal

    2009-05-01

    Based on the rigorous generalized Mie theory solution of Maxwell's equations for dielectric cylinders we theoretically investigate the optical properties of two-dimensional deterministic structures based on the Fibonacci, Thue-Morse and Rudin-Shapiro aperiodic sequences. In particular, we investigate bandgap formation and mode localization properties in aperiodic photonic structures based on the accurate calculation of their local density of states (LDOS). In addition, we explore the potential of photonic structures based on aperiodic order for the engineering of radiative rates and emission patterns in erbium-doped silicon-rich nitride photonic structures.

  6. Influence of aperiodic modulations on first-order transitions: Numerical study of the two-dimensional Potts model

    Science.gov (United States)

    Girardi, D.; Branco, N. S.

    2011-06-01

    We study the Potts model on a rectangular lattice with aperiodic modulations in its interactions along one direction. Numerical results are obtained using the Wolff algorithm and for many lattice sizes, allowing for a finite-size scaling analyses to be carried out. Three different self-dual aperiodic sequences are employed, which leads to more precise results, since the exact critical temperature is known. We analyze two models, with 6 and 15 number of states: both present first-order transitions on their uniform versions. We show that the Harris-Luck criterion, originally introduced in the study of continuous transitions, is obeyed also for first-order ones. Also, we show that the new universality class that emerges for relevant aperiodic modulations depends on the number of states of the Potts model, as obtained elsewhere for random disorder, and on the aperiodic sequence. We determine the occurrence of log-periodic behavior, as expected for models with aperiodic modulated interactions.

  7. Influence of aperiodic modulations on first-order transitions: numerical study of the two-dimensional Potts model.

    Science.gov (United States)

    Girardi, D; Branco, N S

    2011-06-01

    We study the Potts model on a rectangular lattice with aperiodic modulations in its interactions along one direction. Numerical results are obtained using the Wolff algorithm and for many lattice sizes, allowing for a finite-size scaling analyses to be carried out. Three different self-dual aperiodic sequences are employed, which leads to more precise results, since the exact critical temperature is known. We analyze two models, with 6 and 15 number of states: both present first-order transitions on their uniform versions. We show that the Harris-Luck criterion, originally introduced in the study of continuous transitions, is obeyed also for first-order ones. Also, we show that the new universality class that emerges for relevant aperiodic modulations depends on the number of states of the Potts model, as obtained elsewhere for random disorder, and on the aperiodic sequence. We determine the occurrence of log-periodic behavior, as expected for models with aperiodic modulated interactions.

  8. Lyapunov exponents for one-dimensional aperiodic photonic bandgap structures

    Science.gov (United States)

    Kissel, Glen J.

    2011-10-01

    Existing in the "gray area" between perfectly periodic and purely randomized photonic bandgap structures are the socalled aperoidic structures whose layers are chosen according to some deterministic rule. We consider here a onedimensional photonic bandgap structure, a quarter-wave stack, with the layer thickness of one of the bilayers subject to being either thin or thick according to five deterministic sequence rules and binary random selection. To produce these aperiodic structures we examine the following sequences: Fibonacci, Thue-Morse, Period doubling, Rudin-Shapiro, as well as the triadic Cantor sequence. We model these structures numerically with a long chain (approximately 5,000,000) of transfer matrices, and then use the reliable algorithm of Wolf to calculate the (upper) Lyapunov exponent for the long product of matrices. The Lyapunov exponent is the statistically well-behaved variable used to characterize the Anderson localization effect (exponential confinement) when the layers are randomized, so its calculation allows us to more precisely compare the purely randomized structure with its aperiodic counterparts. It is found that the aperiodic photonic systems show much fine structure in their Lyapunov exponents as a function of frequency, and, in a number of cases, the exponents are quite obviously fractal.

  9. Analytical and numerical studies of disordered spin-1 Heisenberg chains with aperiodic couplings

    Science.gov (United States)

    Casa Grande, H. L.; Laflorencie, N.; Alet, F.; Vieira, A. P.

    2014-04-01

    We investigate the low-temperature properties of the one-dimensional spin-1 Heisenberg model with geometric fluctuations induced by aperiodic but deterministic coupling distributions, involving two parameters. We focus on two aperiodic sequences, the Fibonacci sequence and the 6-3 sequence. Our goal is to understand how these geometric fluctuations modify the physics of the (gapped) Haldane phase, which corresponds to the ground state of the uniform spin-1 chain. We make use of different adaptations of the strong-disorder renormalization-group (SDRG) scheme of Ma, Dasgupta, and Hu, widely employed in the study of random spin chains, supplemented by quantum Monte Carlo and density-matrix renormalization-group numerical calculations, to study the nature of the ground state as the coupling modulation is increased. We find no phase transition for the Fibonacci chain, while we show that the 6-3 chain exhibits a phase transition to a gapless, aperiodicity-dominated phase similar to the one found for the aperiodic spin-1/2 XXZ chain. Contrary to what is verified for random spin-1 chains, we show that different adaptations of the SDRG scheme may lead to different qualitative conclusions about the nature of the ground state in the presence of aperiodic coupling modulations.

  10. Garbage Collection Scheduling of Aperiodic Tasks

    Institute of Scientific and Technical Information of China (English)

    Ning Zhang; Guang-Ze Xiong

    2009-01-01

    In the previous work of garbage collection (GC) models, scheduling analysis was given based on an assumption that there were no aperiodic mutator tasks. However, it is not true in practical real-time systems. The GC algorithm which can schedule aperiodic tasks is proposed, and the variance of live memory is analyzed. In this algorithm, active tasks are deferred to be processed by GC until the states of tasks become inactive, and the saved sporadic server time can be used to schedule aperiodic tasks. Scheduling the sample task sets demonstrates that this algorithm in this paper can schedule aperiodic tasks and decrease GC work. Thus, the GC algorithm proposed is more flexible and portable.

  11. Development of Symmetry Concepts for Aperiodic Crystals

    Directory of Open Access Journals (Sweden)

    Ted Janssen

    2014-03-01

    Full Text Available An overview is given of the use of symmetry considerations for aperiodic crystals. Superspace groups were introduced in the seventies for the description of incommensurate modulated phases with one modulation vector. Later, these groups were also used for quasi-periodic crystals of arbitrary rank. Further extensions use time reversal and time translation operations on magnetic and electrodynamic systems. An alternative description of magnetic structures to that with symmetry groups, the Shubnikov groups, is using representations of space groups. The same can be done for aperiodic crystals. A discussion of the relation between the two approaches is given. Representations of space groups and superspace groups play a role in the study of physical properties. These, and generalizations of them, are discussed for aperiodic crystals. They are used, in particular, for the characterization of phase transitions between aperiodic crystal phases.

  12. Triangular dissections, aperiodic tilings and Jones algebras

    CERN Document Server

    Coquereaux, Robert

    1994-01-01

    The Brattelli diagram associated with a given bicolored Dynkin-Coxeter graph of type A_n determines planar fractal sets obtained by infinite dissections of a given triangle. All triangles appearing in the dissection process have angles that are multiples of \\pi/ (n+1). There are usually several possible infinite dissections compatible with a given n but a given one makes use of n/2 triangle types if n is even. Jones algebra with index [ 4 \\ \\cos^2{\\pi \\over n+1}]^{-1} (values of the discrete range) act naturally on vector spaces associated with those fractal sets. Triangles of a given type are always congruent at each step of the dissection process. In the particular case n=4, there are isometric and the whole structure lead, after proper inflation, to aperiodic Penrose tilings. The other "tilings" associated with other values of the index are discussed and shown to be encoded by equivalence classes of infinite sequences (with appropriate constraints) using only n/2 digits (if n is even) and generalizing the ...

  13. Numerical study of Potts models with aperiodic modulations: influence on first-order transitions

    Science.gov (United States)

    Branco, Nilton; Girardi, Daniel

    2012-02-01

    We perform a numerical study of Potts models on a rectangular lattice with aperiodic interactions along one spatial direction. The number of states q is such that the transition is a first-order one for the uniform model. The Wolff algorithm is employed, for many lattice sizes, allowing for a finite-size scaling analyses to be carried out. Three different self-dual aperiodic sequences are employed, such that the exact critical temperature is known: this leads to precise results for the exponents. We analyze models with q=6 and 15 and show that the Harris-Luck criterion, originally introduced in the study of continuous transitions, is obeyed also for first-order ones. The new universality class that emerges for relevant aperiodic modulations depends on the number of states of the Potts model, as obtained elsewhere for random disorder, and on the aperiodic sequence. We determine the occurrence of log-periodic behavior, as expected for models with aperiodic modulated interactions.

  14. Nonclassical properties of electronic states of aperiodic chains in a homogeneous electric field

    Science.gov (United States)

    Spisak, B. J.; Wołoszyn, M.

    2009-07-01

    The electronic energy levels of one-dimensional aperiodic systems driven by a homogeneous electric field are studied by means of a phase-space description based on the Wigner distribution function. The formulation provides physical insight into the quantum nature of the electronic states for the aperiodic systems generated by the Fibonacci and Thue-Morse sequences. The nonclassical parameter for electronic states is studied as a function of the magnitude of homogeneous electric field to achieve the main result of this work, which is to prove that the nonclassical properties of the electronic states in the aperiodic systems determine the transition probability between electronic states in the region of anticrossings. The localization properties of electronic states and the uncertainty product of momentum and position variables are also calculated as functions of the electric field.

  15. Fractal signatures in the aperiodic Fibonacci grating.

    Science.gov (United States)

    Verma, Rupesh; Banerjee, Varsha; Senthilkumaran, Paramasivam

    2014-05-01

    The Fibonacci grating (FbG) is an archetypal example of aperiodicity and self-similarity. While aperiodicity distinguishes it from a fractal, self-similarity identifies it with a fractal. Our paper investigates the outcome of these complementary features on the FbG diffraction profile (FbGDP). We find that the FbGDP has unique characteristics (e.g., no reduction in intensity with increasing generations), in addition to fractal signatures (e.g., a non-integer fractal dimension). These make the Fibonacci architecture potentially useful in image forming devices and other emerging technologies.

  16. Binary supergratings: Aperiodic optics for spectral engineering

    Science.gov (United States)

    Fay, Martin Freestone

    The Binary Supergrating (BSG) is an aperiodic guided-wave optical device which, in parallel to the much-touted Photonic Band Gap, represents the extension of the Bragg grating into frequency space. The result is an easily manufactured two-level refractive index profile offering fully customizable spectral characteristics, including wavelength-dependent control over beam direction, dispersion and power. As a general concept, a BSG can be synthesized using a variety of approaches, ranging from a simple threshold quantization of the emulated ideal analog index profile to more sophisticated delta-sigma modulator (DSM) methods, which preserve diffraction characteristics over a specified band of interest with high fidelity. The comparative advantages of each are explored in the context of their tolerance to manufacturing variances. For most cases, the BSG designs degrade gracefully and retain their functionality under extreme errors in fabrication. However, particular vulnerabilities do emerge, along with strategies to mitigate their effect. The BSG is then demonstrated experimentally, in a first proof-of-concept embodiment employing a lateral satellite grating configuration, which eases fabrication by having both waveguide and grating features defined in the same lithographic sequence. Results from this passive optical device corroborate both the BSG's design flexibility and its particular vulnerabilities, yielding clear directions for subsequent implementations. In the domain of active BSG-enabled devices, the novel self-collimated multi-wavelength laser (SCMWL) outputs low-divergence beams at multiple simultaneous wavelengths. The concept, theory, and design of this invention is presented, followed by experimental results from optically pumped proof-of-concept embodiments. The observed spectra confirm the SCMWL concept, while also revealing the complex dynamics underlying this device. At once simple and subtle, the BSG concept yields itself both for immediate

  17. Optimal design of aperiodic, vertical silicon nanowire structures for photovoltaics.

    Science.gov (United States)

    Lin, Chenxi; Povinelli, Michelle L

    2011-09-12

    We design a partially aperiodic, vertically-aligned silicon nanowire array that maximizes photovoltaic absorption. The optimal structure is obtained using a random walk algorithm with transfer matrix method based electromagnetic forward solver. The optimal, aperiodic structure exhibits a 2.35 times enhancement in ultimate efficiency compared to its periodic counterpart. The spectral behavior mimics that of a periodic array with larger lattice constant. For our system, we find that randomly-selected, aperiodic structures invariably outperform the periodic array.

  18. Dispersion blue-shift in an aperiodic Bragg reflection waveguide

    CERN Document Server

    Fesenko, Volodymyr I

    2016-01-01

    A particular feature of an aperiodic design of cladding of Bragg reflection waveguides to demonstrate a dispersion blue-shift is elucidated. It is made on the basis of a comparative study of dispersion characteristics of both periodic and aperiodic configurations of Bragg mirrors in the waveguide system, wherein for the aperiodic configuration three procedures for layers alternating, namely Fibonacci, Thue-Morse and Kolakoski substitutional rules are considered. It was found out that, in a Bragg reflection waveguide with any considered aperiodic cladding, dispersion curves of guided modes appear to be shifted to shorter wavelengths compared to the periodic configuration regardless of the modes polarization.

  19. Aperiodic structures in condensed matter fundamentals and applications

    CERN Document Server

    Macia Barber, Enrique

    2008-01-01

    One of the Top Selling Physics Books according to YBP Library ServicesOrder can be found in all the structures unfolding around us at different scales, including in the arrangements of matter and in energy flow patterns. Aperiodic Structures in Condensed Matter: Fundamentals and Applications focuses on a special kind of order referred to as aperiodic order.The book covers several topics dealing with the role of aperiodic order in numerous domains of the physical sciences and technology. It first presents the most characteristic features of various aperiodic systems. The author then describes t

  20. Low-Energy Electron Diffraction (LEED) Study of an Aperiodic Thin Film of Cu on 5-fold i-Al-Pd-Mn

    OpenAIRE

    Pussi, Katariina; Reid, Dennis; Ferralis, Nicola; McGrath, Ronan; Lograsso, Thomas; Ross, Amy; Diehl, Renee

    2008-01-01

    Abstract Thin films of copper grown on 5-fold i-AlPdMn at room temperature consist of domains that are rotationally aligned with the five primary symmetry directions of the substrate and which have one-dimensional aperiodic order. This aperiodic order is evident in scanning tunneling microscopy (STM) images as wide and narrow rows that are spaced according to a Fibonacci sequence. A low-energy electron diffraction (LEED) study of this film indicates that the structure within the ...

  1. Finite current stationary states of random walks on one-dimensional lattices with aperiodic disorder

    Science.gov (United States)

    Miki, Hiroshi

    2016-11-01

    Stationary states of random walks with finite induced drift velocity on one-dimensional lattices with aperiodic disorder are investigated by scaling analysis. Three aperiodic sequences, the Thue-Morse (TM), the paperfolding (PF), and the Rudin-Shapiro (RS) sequences, are used to construct the aperiodic disorder. These are binary sequences, composed of two symbols A and B, and the ratio of the number of As to that of Bs converges to unity in the infinite sequence length limit, but their effects on diffusional behavior are different. For the TM model, the stationary distribution is extended, as in the case without current, and the drift velocity is independent of the system size. For the PF model and the RS model, as the system size increases, the hierarchical and fractal structure and the localized structure, respectively, are broken by a finite current and changed to an extended distribution if the system size becomes larger than a certain threshold value. Correspondingly, the drift velocity is saturated in a large system while in a small system it decreases as the system size increases.

  2. Overlap amplitude and localization properties in aperiodic diluted and non-diluted direct electric transmission lines

    Science.gov (United States)

    Lazo, E.; Castro, C. E.; Cortés-Cortés, F.

    2016-09-01

    In this work we study the relationship existing between the localization properties of the diluted and non-diluted direct electrical transmission lines with the overlap amplitude Cijω = 2 | Iiω Ijω | , where Ijω is the amplitude of the electric current function at jth cell of the transmission line for the state with frequency ω. We distribute two values of inductances LA and LB, according to the generalized aperiodic Thue-Morse m-tupling sequence. We find that the behavior of Ci,jω is directly related to the localization properties of the aperiodic sequences measured by the ξ normalized participation number, the Rq Rényi entropies and the μq moments. In addition, we generalize the scaling relationship for the overlap amplitude Ci,jω, i.e., =(2/N) 2 q.

  3. Polaritonic excitations in aperiodic nanolayers

    Science.gov (United States)

    Vasconcelos, M. S.; Anselmo, Dory Hélio A. L.; Mello, Vamberto D.

    2014-03-01

    The magnetic polariton propagation in magnonic layered structures is theoretically studied by using a a transfer matrix approach. The layered structures considered here are made up by the periodic and quasiperiodic stacking of two different layers (also known as building blocks, named A and B), where one of them is a ferromagnetic nanofilm (A), while the other is a metamaterial nanolayer (B). For the periodic arrangement, the bulk modes are characterized by two large symmetric bands, with non-reciprocal surface modes between them. The quasiperiodic metamagnetic structure is then built up by following the Fibonacci sequence, whose long range order effect is then investigated, giving rise to an interesting self-similar spectra.

  4. Three-Distance Sequences with Three Symbols

    OpenAIRE

    SAKAMOTO, Kuniko

    2003-01-01

    We will show that every $3$ dimensional cutting sequence is a three-distance sequence, and there are uncountable many periodic or aperiodic three-distance sequences (with $3$-symbols) which are not $3$ dimensional cutting sequences.

  5. Electronic properties of aperiodic quantum dot chains

    Science.gov (United States)

    Korotaev, P. Yu.; Vekilov, Yu. Kh.; Kaputkina, N. E.

    2012-04-01

    The electronic spectral and transport properties of aperiodic quantum dot chains are investigated. The systems with singular continuous energy spectrum are considered: Thue-Morse chain, double-periodic chain, Rudin-Shapiro chain. The influence of electronic energy in quantum dot on the spectral properties, band structure, density of states and spectral resistivity, is discussed. Low resistivity regions correspond to delocalized states and these states could be current states. Also we discuss the magnetic field application as the way to tune electronic energy in quantum dot and to obtain metallic or insulating conducting states of the systems.

  6. Periodic and Aperiodic Synchronization in Skilled Action

    Science.gov (United States)

    Cummins, Fred

    2011-01-01

    Synchronized action is considered as a manifestation of shared skill. Most synchronized behaviors in humans and other animals are based on periodic repetition. Aperiodic synchronization of complex action is found in the experimental task of synchronous speaking, in which naive subjects read a common text in lock step. The demonstration of synchronized behavior without a periodic basis is presented as a challenge for theoretical understanding. A unified treatment of periodic and aperiodic synchronization is suggested by replacing the sequential processing model of cognitivist approaches with the more local notion of a task-specific sensorimotor coordination. On this view, skilled action is the imposition of constraints on the co-variation of movement and sensory flux such that the boundary conditions that define the skill are met. This non-cognitivist approach originates in the work of John Dewey. It allows a unification of the treatment of sensorimotor synchronization in simple rhythmic behavior and in complex skilled behavior and it suggests that skill sharing is a uniquely human trait of considerable import. PMID:22232583

  7. Periodic and aperiodic synchronization in skilled action

    Directory of Open Access Journals (Sweden)

    Fred eCummins

    2011-12-01

    Full Text Available Synchronized action is considered as a manifestation of shared skill. Most synchronized behaviors in humans and other animals are based on periodic repetition. Aperiodic synchronization of complex action is found in the experimental task of synchronous speaking, in which naive subjects read a common text in lock step. The demonstration of synchronized behavior without a periodic basis is presented as a challenge for theoretical understanding. A unified treatment of periodic and aperiodic synchronization is suggested by replacing the sequential processing model of cognitivist approaches with the more local notion of a task-specific sensorimotor coordination. On this view, skilled action is the imposition of constraints on the co-variation of movement and sensory flux such that the boundary conditions that define the skill are met. This non-cognitivist approach originates in the work of John Dewey. It allows a unification of the treatment of sensorimotor synchronization in simple rhythmic behavior and in complex skilled behavior and it suggests that skill sharing is a uniquely human trait of considerable import.

  8. Can fractal-like spectra be experimentally observed in aperiodic superlattices?

    Science.gov (United States)

    Maciá, Enrique; Domínguez-Adame, Francisco

    1996-07-01

    We numerically investigate the effects of inhomogeneities in the energy spectrum of aperiodic semiconductor superlattices, focusing our attention on Thue-Morse and Fibonacci sequences. In the absence of disorder, the corresponding electronic spectra are self-similar. The presence of a certain degree of randomness, due to imperfections occurring during the growth processes, gives rise to a progressive loss of quantum coherence, smearing out the finer details of the energy spectra predicted for perfect aperiodic superlattices and spurring the onset of electron localization. However, depending on the degree of disorder introduced, a critical size for the system exists, below which peculiar transport properties, related to the pre-fractal nature of the energy spectrum, may be measured.

  9. [Comfort after a sad outcome of pregnancy. Two letters of Frederick the Great to Wilhelmina of Prussia].

    Science.gov (United States)

    Lammes, Frits B; Walvoort, Henk C

    2009-01-01

    After her unfortunate experience of parturition Princess Wilhelmina of Prussia, married to stadhouder Prince Willem V, received two letters of comfort from her beloved godfather King Frederick II (Frederick the Great) of Prussia. These letters illustrate the special close connection there was between them. The letters also give a view on the difficult question of giving comfort after perinatal death.

  10. Hidden degrees of freedom in aperiodic materials.

    Science.gov (United States)

    Toudic, Bertrand; Garcia, Pilar; Odin, Christophe; Rabiller, Philippe; Ecolivet, Claude; Collet, Eric; Bourges, Philippe; McIntyre, Garry J; Hollingsworth, Mark D; Breczewski, Tomasz

    2008-01-04

    Numerous crystalline materials, including those of bioorganic origin, comprise incommensurate sublattices whose mutual arrangement is described in a superspace framework exceeding three dimensions. We report direct observation by neutron diffraction of superspace symmetry breaking in a solid-solid phase transition of an incommensurate host-guest system: the channel inclusion compound of nonadecane/urea. Strikingly, this phase transition generates a unit cell doubling that concerns only the modulation of one substructure by the other-an internal variable available only in superspace. This unanticipated pathway for degrees of freedom to rearrange leads to a second phase transition, which again is controlled by the higher dimensionality of superspace. These results reveal nature's capacity to explore the increased number of phases allowed in aperiodic crystals.

  11. Phase-coded pulse aperiodic transmitter coding

    Directory of Open Access Journals (Sweden)

    I. I. Virtanen

    2009-07-01

    Full Text Available Both ionospheric and weather radar communities have already adopted the method of transmitting radar pulses in an aperiodic manner when measuring moderately overspread targets. Among the users of the ionospheric radars, this method is called Aperiodic Transmitter Coding (ATC, whereas the weather radar users have adopted the term Simultaneous Multiple Pulse-Repetition Frequency (SMPRF. When probing the ionosphere at the carrier frequencies of the EISCAT Incoherent Scatter Radar facilities, the range extent of the detectable target is typically of the order of one thousand kilometers – about seven milliseconds – whereas the characteristic correlation time of the scattered signal varies from a few milliseconds in the D-region to only tens of microseconds in the F-region. If one is interested in estimating the scattering autocorrelation function (ACF at time lags shorter than the F-region correlation time, the D-region must be considered as a moderately overspread target, whereas the F-region is a severely overspread one. Given the technical restrictions of the radar hardware, a combination of ATC and phase-coded long pulses is advantageous for this kind of target. We evaluate such an experiment under infinitely low signal-to-noise ratio (SNR conditions using lag profile inversion. In addition, a qualitative evaluation under high-SNR conditions is performed by analysing simulated data. The results show that an acceptable estimation accuracy and a very good lag resolution in the D-region can be achieved with a pulse length long enough for simultaneous E- and F-region measurements with a reasonable lag extent. The new experiment design is tested with the EISCAT Tromsø VHF (224 MHz radar. An example of a full D/E/F-region ACF from the test run is shown at the end of the paper.

  12. Critical behavior of the Ising model on a hierarchical lattice with aperiodic interactions

    Science.gov (United States)

    Pinho, S. T. R.; Haddad, T. A. S.; Salinas, S. R.

    We write the exact renormalization-group recursion relations for nearest-neighbor ferromagnetic Ising models on Migdal-Kadanoff hierarchical lattices with a distribution of aperiodic exchange interactions according to a class of substitutional sequences. For small geometric fluctuations, the critical behavior is unchanged with respect to the uniform case. For large fluctuations, as in the case of the Rudin-Shapiro sequence, the uniform fixed point in the parameter space cannot be reached from any physical initial conditions. We derive a criterion to check the relevance of the geometric fluctuations.

  13. Smith-Purcell radiation emission in aperiodic arrays

    Science.gov (United States)

    Saavedra, J. R. M.; Castells-Graells, D.; García de Abajo, F. Javier

    2016-07-01

    We study the Smith-Purcell light emission produced by electrons moving parallel to linear aperiodic particle arrays. This constitutes a generalization of this type of phenomenon from periodic to aperiodic structures. As in the periodic case, the emission is found to exhibit intense features in its angular and frequency distributions, associated with the condition of constructive interference between the contributions arising from different particles in the array. This condition can also be expressed in terms of momentum conservation involving reciprocal wave-vector transfers from the array. We consider two examples of quasiperiodic and hyperuniform aperiodic arrays that allow us to illustrate this idea. Our study provides insight into the interaction of fast electrons with aperiodic arrays characterized by strong features in reciprocal space, which dominate the electron-array coupling.

  14. New construction of hybrid and aperiodic ordered PBG cavity

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    The band gap of a photonic crystal (PhC) cavity intrinsically avoids HOM problems. In this paper, we present a new PBG structure based on the possible advantage of using hybrid structures and aperiodic lattices. This novel hybrid and aperiodically ordered cavity was designed for apparently higher Q-factor (more than 10300) and achieving large accelerating field gradient. The HOMs in the cavity are able to be absorbed efficiently.

  15. Nonuniversal behavior for aperiodic interactions within a mean-field approximation.

    Science.gov (United States)

    Faria, Maicon S; Branco, N S; Tragtenberg, M H R

    2008-04-01

    We study the spin-1/2 Ising model on a Bethe lattice in the mean-field limit, with the interaction constants following one of two deterministic aperiodic sequences, the Fibonacci or period-doubling one. New algorithms of sequence generation were implemented, which were fundamental in obtaining long sequences and, therefore, precise results. We calculate the exact critical temperature for both sequences, as well as the critical exponents beta, gamma, and delta . For the Fibonacci sequence, the exponents are classical, while for the period-doubling one they depend on the ratio between the two exchange constants. The usual relations between critical exponents are satisfied, within error bars, for the period-doubling sequence. Therefore, we show that mean-field-like procedures may lead to nonclassical critical exponents.

  16. Applications the Lagrangian description in aperiodic flows

    Science.gov (United States)

    Mendoza, Carolina; Mancho, Ana Maria

    2012-11-01

    We use several recently developed Lagrangian tools for describing transport in general aperiodic flows. In our approach the first step is based in a Lagrangian descriptor (the so called function M). It measures the length of particle trajectories on the ocean surface over a given interval of time. We describe its output over satellite altimetry data on the Kuroshio current. The technique is combined with the direct computation of manifolds of Distinguished Hyperbolic trajectories and a very detailed description of transport is achieved across an eddy and a jet on the Kuroshio current,. A second velocity data set is examined with the M function tool. These are obtained from the HYCOM project on the Gulf of Mexico during the time of the oil-spill. We have identified underlying Lagrangian structures and dynamics. We acknowledge to the hospitality of the university of Delaware and the assistance of Bruce Lipphardt and Helga Huntley in accessing the model data sets. We acknowledge to the grants: UPM-AL12-PAC-09, Becas de Movilidad de Caja Madrid 2011, MTM2011-26696 and ILINK-0145.

  17. Elastic wave localization in two-dimensional phononic crystals with one-dimensional random disorder and aperiodicity

    Science.gov (United States)

    Yan, Zhi-Zhong; Zhang, Chuanzeng; Wang, Yue-Sheng

    2011-03-01

    The band structures of in-plane elastic waves propagating in two-dimensional phononic crystals with one-dimensional random disorder and aperiodicity are analyzed in this paper. The localization of wave propagation is discussed by introducing the concept of the localization factor, which is calculated by the plane-wave-based transfer-matrix method. By treating the random disorder and aperiodicity as the deviation from the periodicity in a special way, three kinds of aperiodic phononic crystals that have normally distributed random disorder, Thue-Morse and Rudin-Shapiro sequence in one direction and translational symmetry in the other direction are considered and the band structures are characterized using localization factors. Besides, as a special case, we analyze the band gap properties of a periodic planar layered composite containing a periodic array of square inclusions. The transmission coefficients based on eigen-mode matching theory are also calculated and the results show the same behaviors as the localization factor does. In the case of random disorders, the localization degree of the normally distributed random disorder is larger than that of the uniformly distributed random disorder although the eigenstates are both localized no matter what types of random disorders, whereas, for the case of Thue-Morse and Rudin-Shapiro structures, the band structures of Thue-Morse sequence exhibit similarities with the quasi-periodic (Fibonacci) sequence not present in the results of the Rudin-Shapiro sequence.

  18. Simulated Performance of Timescale Metrics for Aperiodic Light Curves

    CERN Document Server

    Findeisen, Krzysztof; Hillenbrand, Lynne

    2014-01-01

    Aperiodic variability is a characteristic feature of young stars, massive stars, and active galactic nuclei. With the recent proliferation of time domain surveys, it is increasingly essential to develop methods to quantify and analyze aperiodic variability. We develop three timescale metrics that have been little used in astronomy -- {\\Delta}m-{\\Delta}t plots, peak-finding, and Gaussian process regression -- and present simulations comparing their effectiveness across a range of aperiodic light curve shapes, characteristic timescales, observing cadences, and signal to noise ratios. We find that Gaussian process regression is easily confused by noise and by irregular sampling, even when the model being fit reflects the process underlying the light curve, but that {\\Delta}m-{\\Delta}t plots and peak-finding can coarsely characterize timescales across a broad region of parameter space. We make public the software we used for our simulations, both in the spirit of open research and to allow others to carry out ana...

  19. Structural and Spectral Properties of Deterministic Aperiodic Optical Structures

    Directory of Open Access Journals (Sweden)

    Luca Dal Negro

    2016-12-01

    Full Text Available In this comprehensive paper we have addressed structure-property relationships in a number of representative systems with periodic, random, quasi-periodic and deterministic aperiodic geometry using the interdisciplinary methods of spatial point pattern analysis and spectral graph theory as well as the rigorous Green’s matrix method, which provides access to the electromagnetic scattering behavior and spectral fluctuations (distributions of complex eigenvalues as well as of their level spacing of deterministic aperiodic optical media for the first time.

  20. Optical induction scheme for assembling nondiffracting aperiodic Vogel spirals

    Energy Technology Data Exchange (ETDEWEB)

    Diebel, Falko, E-mail: falko.diebel@uni-muenster.de; Rose, Patrick; Boguslawski, Martin; Denz, Cornelia [Institut für Angewandte Physik and Center for Nonlinear Science (CeNoS), Westfälische Wilhelms-Universität Münster, 48149 Münster (Germany)

    2014-05-12

    We introduce an experimental approach to realize aperiodic photonic lattices based on multiplexing of nondiffracting Bessel beams. This holographic optical induction scheme takes advantage of the well localized Bessel beam as a basis to assemble two-dimensional photonic lattices. We present the realization of an optically induced two-dimensional golden-angle Vogel spiral lattice, which belongs to the family of deterministic aperiodic structures. With our technique, a very broad class of photonic refractive index landscapes now becomes accessible to optical induction, which could not be realized with established distributed holographic techniques.

  1. Anisotropic Heisenberg model on hierarchical lattices with aperiodic interactions: a renormalization-group approach.

    Science.gov (United States)

    Branco, N S; de Sousa, J Ricardo; Ghosh, Angsula

    2008-03-01

    Using a real-space renormalization-group approximation, we study the anisotropic quantum Heisenberg model on hierarchical lattices, with interactions following aperiodic sequences. Three different sequences are considered, with relevant and irrelevant fluctuations, according to the Luck-Harris criterion. The phase diagram is discussed as a function of the anisotropy parameter Delta (such that Delta=0 and 1 correspond to the isotropic Heisenberg and Ising models, respectively). We find three different types of phase diagrams, with general characteristics: the isotropic Heisenberg plane is always an invariant one (as expected by symmetry arguments) and the critical behavior of the anisotropic Heisenberg model is governed by fixed points on the Ising-model plane. Our results for the isotropic Heisenberg model show that the relevance or irrelevance of aperiodic models, when compared to their uniform counterpart, is as predicted by the Harris-Luck criterion. A low-temperature renormalization-group procedure was applied to the classical isotropic Heisenberg model in two-dimensional hierarchical lattices: the relevance criterion is obtained, again in accordance with the Harris-Luck criterion.

  2. Effect of aperiodicity on the broadband reflection of silicon nanorod structures for photovoltaics.

    Science.gov (United States)

    Lin, Chenxi; Huang, Ningfeng; Povinelli, Michelle L

    2012-01-02

    We carry out a systematic numerical study of the effects of aperiodicity on silicon nanorod anti-reflection structures. We use the scattering matrix method to calculate the average reflection loss over the solar spectrum for periodic and aperiodic arrangements of nanorods. We find that aperiodicity can either improve or deteriorate the anti-reflection performance, depending on the nanorod diameter. We use a guided random-walk algorithm to design optimal aperiodic structures that exhibit lower reflection loss than both optimal periodic and random aperiodic structures.

  3. Aperiodic Multiprocessor Scheduling for Real-Time Stream Processing Applications

    NARCIS (Netherlands)

    Wiggers, M.H.

    2009-01-01

    This thesis is concerned with the computation of buffer capacities that guarantee satisfaction of timing and resource constraints for task graphs with aperiodic task execution rates that are executed on run-time scheduled resources. Stream processing applications such as digital radio baseband proce

  4. Aperiodic Multiprocessor Scheduling for Real-Time Stream Processing Applications

    NARCIS (Netherlands)

    Wiggers, M.H.

    2009-01-01

    This thesis is concerned with the computation of buffer capacities that guarantee satisfaction of timing and resource constraints for task graphs with aperiodic task execution rates that are executed on run-time scheduled resources. Stream processing applications such as digital radio baseband

  5. Bloch oscillations in an aperiodic one-dimensional potential

    NARCIS (Netherlands)

    de Moura, FABF; Lyra, ML; Dominguez-Adame, F; Malyshev, V.A.

    2005-01-01

    We study the dynamics of an electron subjected to a static uniform electric field within a one-dimensional tight-binding model with a slowly varying aperiodic potential. The unbiased model is known to support phases of localized and extended one-electron states separated by two mobility edges. We sh

  6. Wave propagation in one-dimensional solid-fluid quasi-periodic and aperiodic phononic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Chen Ali, E-mail: alchen@bjtu.edu.cn [Institute of Engineering Mechanics, Beijing Jiaotong University, Beijing 100044 (China); Wang Yuesheng [Institute of Engineering Mechanics, Beijing Jiaotong University, Beijing 100044 (China); Zhang Chuanzeng [Department of Civil Engineering, University of Siegen, D-57068 Siegen (Germany)

    2012-02-01

    The propagation of the elastic waves in one-dimensional (1D) solid-fluid quasi-periodic phononic crystals is studied by employing the concept of the localization factor, which is calculated by the transfer matrix method. The solid-fluid interaction effect at the interfaces between the solid and the fluid components is considered. For comparison, the periodic systems and aperiodic Thue-Morse sequence are also analyzed in this paper. The splitting phenomenon of the pass bands and bandgaps are discussed for these 1D solid-fluid systems. At last the influences of the material impedance ratios on the band structures of the 1D solid-fluid quasi-periodic phononic crystals arranged as Fibonacci sequence are discussed.

  7. High-pressure crystallography of periodic and aperiodic crystals.

    Science.gov (United States)

    Hejny, Clivia; Minkov, Vasily S

    2015-03-01

    More than five decades have passed since the first single-crystal X-ray diffraction experiments at high pressure were performed. These studies were applied historically to geochemical processes occurring in the Earth and other planets, but high-pressure crystallography has spread across different fields of science including chemistry, physics, biology, materials science and pharmacy. With each passing year, high-pressure studies have become more precise and comprehensive because of the development of instrumentation and software, and the systems investigated have also become more complicated. Starting with crystals of simple minerals and inorganic compounds, the interests of researchers have shifted to complicated metal-organic frameworks, aperiodic crystals and quasicrystals, molecular crystals, and even proteins and viruses. Inspired by contributions to the microsymposium 'High-Pressure Crystallography of Periodic and Aperiodic Crystals' presented at the 23rd IUCr Congress and General Assembly, the authors have tried to summarize certain recent results of single-crystal studies of molecular and aperiodic structures under high pressure. While the selected contributions do not cover the whole spectrum of high-pressure research, they demonstrate the broad diversity of novel and fascinating results and may awaken the reader's interest in this topic.

  8. Intrinsic periodic and aperiodic stochastic resonance in an electrochemical cell

    Science.gov (United States)

    Tiwari, Ishant; Phogat, Richa; Parmananda, P.; Ocampo-Espindola, J. L.; Rivera, M.

    2016-08-01

    In this paper we show the interaction of a composite of a periodic or aperiodic signal and intrinsic electrochemical noise with the nonlinear dynamics of an electrochemical cell configured to study the corrosion of iron in an acidic media. The anodic voltage setpoint (V0) in the cell is chosen such that the anodic current (I ) exhibits excitable fixed point behavior in the absence of noise. The subthreshold periodic (aperiodic) signal consists of a train of rectangular pulses with a fixed amplitude and width, separated by regular (irregular) time intervals. The irregular time intervals chosen are of deterministic and stochastic origins. The amplitude of the intrinsic internal noise, regulated by the concentration of chloride ions, is then monotonically increased, and the provoked dynamics are analyzed. The signal to noise ratio and the cross-correlation coefficient versus the chloride ions' concentration curves have a unimodal shape indicating the emergence of an intrinsic periodic or aperiodic stochastic resonance. The abscissa for the maxima of these unimodal curves correspond to the optimum value of intrinsic noise where maximum regularity of the invoked dynamics is observed. In the particular case of the intrinsic periodic stochastic resonance, the scanning electron microscope images for the electrode metal surfaces are shown for certain values of chloride ions' concentrations. These images, qualitatively, corroborate the emergence of order as a result of the interaction between the nonlinear dynamics and the composite signal.

  9. High-pressure crystallography of periodic and aperiodic crystals

    Directory of Open Access Journals (Sweden)

    Clivia Hejny

    2015-03-01

    Full Text Available More than five decades have passed since the first single-crystal X-ray diffraction experiments at high pressure were performed. These studies were applied historically to geochemical processes occurring in the Earth and other planets, but high-pressure crystallography has spread across different fields of science including chemistry, physics, biology, materials science and pharmacy. With each passing year, high-pressure studies have become more precise and comprehensive because of the development of instrumentation and software, and the systems investigated have also become more complicated. Starting with crystals of simple minerals and inorganic compounds, the interests of researchers have shifted to complicated metal–organic frameworks, aperiodic crystals and quasicrystals, molecular crystals, and even proteins and viruses. Inspired by contributions to the microsymposium `High-Pressure Crystallography of Periodic and Aperiodic Crystals' presented at the 23rd IUCr Congress and General Assembly, the authors have tried to summarize certain recent results of single-crystal studies of molecular and aperiodic structures under high pressure. While the selected contributions do not cover the whole spectrum of high-pressure research, they demonstrate the broad diversity of novel and fascinating results and may awaken the reader's interest in this topic.

  10. Generation of broadband and multiple-peak THz radiation in aperiodically poled lithium niobate

    Institute of Scientific and Technical Information of China (English)

    Fucheng Chen; Xianfeng Chen; Yuping Chen; Yuxing Xia

    2005-01-01

    @@ We theoretically analyze the generation of broadened and multi-peak terahertz (THz) radiation in aperiodically poled lithium niobate (APPLN), whose sequence of opposite domains is optimized by simulated annealing (SA) algorithm. The full-width at half maximum (FWHM) of the broadened THz radiation in our simulation is 0.26 THz. Both of the central wavelength and FWHM can be easily tuned by choosing proper objective functions. THz radiation with wider and flatter FWHM can be achieved by increasing the length of the lithium niobate crystal. The two-peak THz generation is also provided as an example of multi-peak with the central wavelengths at 1.68 and 1.80 THz, respectively.

  11. The DNA electronic specific heat at low temperature: The role of aperiodicity

    Energy Technology Data Exchange (ETDEWEB)

    Sarmento, R.G. [Departamento de Física, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN (Brazil); Mendes, G.A. [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN (Brazil); Albuquerque, E.L., E-mail: eudenilson@gmail.com [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN (Brazil); Fulco, U.L. [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN (Brazil); Vasconcelos, M.S. [Escola de Ciências e Tecnologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN (Brazil); Ujsághy, O. [Department of Theoretical Physics and Condensed Matter Research Group of the Hungarian Academy of Sciences, Budapest University of Technology and Economics, Budafoki út 8, H-1521 Budapest (Hungary); Freire, V.N. [Departamento de Física, Universidade Federal do Ceará, 60455-760, Fortaleza, CE (Brazil); Caetano, E.W.S. [Instituto Federal de Educação, Ciência e Tecnologia do Ceará, 60040-531, Fortaleza, CE (Brazil)

    2012-07-16

    The electronic specific heat spectra at constant volume (C{sub V}) of a long-range correlated extended ladder model, mimicking a DNA molecule, is theoretically analyzed for a stacked array of a double-stranded structure made up from the nucleotides guanine G, adenine A, cytosine C and thymine T. The role of the aperiodicity on C{sub V} is discussed, considering two different nucleotide arrangements with increasing disorder, namely the Fibonacci and the Rudin–Shapiro quasiperiodic structures. Comparisons are made for different values of the band fillings, considering also a finite segment of natural DNA, as part of the human chromosome Ch22. -- Highlights: ► Quasiperiodic sequence to mimic the DNA nucleotides arrangement. ► Electronic tight-binding Hamiltonian model. ► Electronic density of states. ► Electronic specific heat spectra.

  12. Engineering aperiodic nanostructured surfaces for scattering-based optical devices

    Science.gov (United States)

    Lee, Yuk Kwan Sylvanus

    Novel optical devices such as biosensors, color displays and authentication devices can be obtained from the distinctive light scattering properties of resonant nanoparticles and nanostructured arrays. These arrays can be optimized through the choice of material, particle morphology and array geometry. In this thesis, by engineering the multi-frequency colorimetric responses of deterministic aperiodic nanostructured surfaces (DANS) with various spectral Fourier properties, I designed, fabricated and characterized scattering-based devices for optical biosensing and structural coloration applications. In particular, using analytical and numerical optimization, colorimetric biosensors are designed and fabricated with conventional electron beam lithography, and characterized using dark-field scattering imaging as well as image autocorrelation analysis of scattered intensity in the visible spectral range. These sensors, which consist of aperiodic surfaces ranging from quasi-periodic to pseudo-random structures with flat Fourier spectra, sustain highly complex structural resonances that enable a novel optical sensing approach beyond the traditional Bragg scattering. To this end, I have experimentally demonstrated that DANS with engineered structural colors are capable of detecting nanoscale protein monolayers with significantly enhanced sensitivity over periodic structures. In addition, different aperiodic arrays of gold (Au) nanoparticles are integrated with polydimethylsiloxane (PDMS) microfluidic structures by soft-lithographic micro-imprint techniques. Distinctive scattering spectral shifts and spatial modifications of structural color patterns in response to refractive index variations were simultaneously measured. The successful integration of DANS with microfluidics technology has introduced a novel opto-fluidic sensing platform for label-free and multiplexed lab-on-a-chip applications. Moreover, by studying the isotropic scattering properties of homogenized

  13. Topological aperiodicity for product systems over semigroups of Ore type

    DEFF Research Database (Denmark)

    Kwasniewski, Bartosz; Szymanski, Wojciech

    2016-01-01

    We prove a version of uniqueness theorem for Cuntz-Pimsner algebras of discrete product systems over semigroups of Ore type. To this end, we introduce Doplicher-Roberts picture of Cuntz-Pimsner algebras, and the semigroup dual to a product system of 'regular' C*-correspondences. Under a certain...... aperiodicity condition on the latter, we obtain the uniqueness theorem and a simplicity criterion for the algebras in question. These results generalize the corresponding ones for crossed products by discrete groups, due to Archbold and Spielberg, and for Exel's crossed products, due to Exel and Vershik...

  14. Experimental demonstration of broadband absorption enhancement in partially aperiodic silicon nanohole structures

    CERN Document Server

    Lin, Chenxi; Povinelli, Michelle L

    2013-01-01

    We report the design, fabrication, and optical absorption measurement of silicon membranes patterned with partially aperiodic nanohole structures. We demonstrate excellent agreement between measurement and simulations. We optimize a partially aperiodic structure using a random walk algorithm and demonstrate an experimental broadband absorption of 4.9 times that of a periodic array.

  15. Extended State to Localization in Random Aperiodic Chains

    Institute of Scientific and Technical Information of China (English)

    GAO Hui-Fen; TAO Rui-Bao

    2006-01-01

    The electronic states in Thus-Morse chain (TMC) and generalized Fibonacci chain (GFC) are studied by solving eigenequation and using transfer matrix method. Two model Hamiltonians are studied. One contains the nearest neighbor (n.n.) hopping terms only and the other has additionally next nearest neighbor (n.n.n.) hopping terms. Based on the transfer matrix method, a criterion of transition from the extended to the localized states is suggested for GFC and TMC. The numerical calculation shows the existence of both extended and localized states in pure aperiodic system. A random potential is introduced to the diagonal term of the Hamiltonian and then the extended states are always changed to be localized. The exponents related to the localization length as a function of randomness are calculated. For different kinds of aperiodic chain, the critical value of randomness for the transition from extended to the localized states are found to be zero, consistent with the case of ordinary one-dimensional systems.

  16. Broadband and omnidirectional light harvesting enhancement in photovoltaic devices with aperiodic TiO2 nanotube photonic crystal

    Science.gov (United States)

    Guo, Min; Su, Haijun; Zhang, Jun; Liu, Lin; Fu, Nianqing; Yong, Zehui; Huang, Haitao; Xie, Keyu

    2017-03-01

    Design of more effective broadband light-trapping elements to improve the light harvesting efficiency under both normal and tilted light for solar cells and other photonic devices is highly desirable. Herein we present a theoretical analysis on the optical properties of a novel TiO2 nanotube aperiodic photonic crystal (NT APC) following an aperiodic sequences and its photocurrent enhancement effect for dye-sensitized solar cells (DSSCs) under various incidence angles. It is found that, compared to regular PC, the designed TiO2 NT APC owns broader reflection region and a desired omnidirectional reflection (ODR) bandgaps, leading to considerable and stable photocurrent enhancement under both normal and oblique light. The effects of the structural parameters of the TiO2 NT APC, including the average lattice constant and the common sequence difference, on the optical properties, ODR bandgaps and absorption magnification of the integrated DSSCs are investigated in detail. Moreover, the angular dependence of photocurrent enhancement and angular compensation effect of such TiO2 NT APCs are also provided to offer a guidance on the optimum structural parameters design under different engineering application conditions.

  17. Mean-field calculation of critical parameters and log-periodic characterization of an aperiodic-modulated model.

    Science.gov (United States)

    Oliveira, T P; Branco, N S

    2012-01-01

    We employ a mean-field approximation to study the Ising model with aperiodic modulation of its interactions in one spatial direction. Two different values for the exchange constant, J(A) and J(B), are present, according to the Fibonacci sequence. We calculate the pseudocritical temperatures for finite systems and extrapolate them to the thermodynamic limit. We explicitly obtain the exponents β, δ, and γ and, from the usual scaling relations for anisotropic models at the upper critical dimension (assumed to be 4 for the model we treat), we calculate α, ν, ν(∥), η, and η(∥). Within the framework of a renormalization-group approach, the Fibonacci sequence is a marginal one and we obtain exponents that depend on the ratio r≡J(B)/J(A), as expected; however, the scaling relation γ=β(δ-1) is obeyed for all values of r we studied. We characterize some thermodynamic functions as log-periodic functions of their arguments, as expected for aperiodic-modulated models, and obtain precise values for the exponents from this characterization.

  18. Dispersion properties of a nanophotonic Bragg waveguide with finite aperiodic cladding

    CERN Document Server

    Fesenko, Volodymyr I; Shulika, Oleksiy V; Sukhoivanov, Igor A

    2015-01-01

    A comprehensive analysis of guided modes of a novel type of a planar Bragg reflection waveguide which consists of a low refractive index guiding layer sandwiched between two finite aperiodic mirrors is presented. The layers in the mirrors are aperiodically arranged according to the Kolakoski substitution rule. In such a waveguide light is confined inside the core by Bragg reflection from the mirrors, while dispersion characteristics of guided modes strongly depend on aperiodicity of the cladding. Using the transfer matrix formalism bandgap conditions, dispersion characteristics and mode profiles of the guided modes of such Bragg reflection waveguide are studied.

  19. Gain modulation by graphene plasmons in aperiodic lattice lasers

    Science.gov (United States)

    Chakraborty, S.; Marshall, O. P.; Folland, T. G.; Kim, Y.-J.; Grigorenko, A. N.; Novoselov, K. S.

    2016-01-01

    Two-dimensional graphene plasmon-based technologies will enable the development of fast, compact, and inexpensive active photonic elements because, unlike plasmons in other materials, graphene plasmons can be tuned via the doping level. Such tuning is harnessed within terahertz quantum cascade lasers to reversibly alter their emission. This is achieved in two key steps: first, by exciting graphene plasmons within an aperiodic lattice laser and, second, by engineering photon lifetimes, linking graphene’s Fermi energy with the round-trip gain. Modal gain and hence laser spectra are highly sensitive to the doping of an integrated, electrically controllable, graphene layer. Demonstration of the integrated graphene plasmon laser principle lays the foundation for a new generation of active, programmable plasmonic metamaterials with major implications across photonics, material sciences, and nanotechnology.

  20. Bias driven coherent carrier dynamics in a two-dimensional aperiodic potential

    NARCIS (Netherlands)

    de Moura, F. A. B. F.; Viana, L. P.; Lyra, M. L.; Malyshev, Victor; Dominguez-Adame, F.

    2008-01-01

    We study the dynamics of an electron wave-packet in a two-dimensional square lattice with an aperiodic site potential in the presence of an external uniform electric field. The aperiodicity is described by epsilon(m) = V cos(pi alpha m(x)(nu x)) cos(pi alpha m(y)(nu y)) at lattice sites (m(x),m(y)),

  1. PERIODIC AND APERIODIC VARIABILITY IN THE MOLECULAR CLOUD ρ OPHIUCHUS

    Energy Technology Data Exchange (ETDEWEB)

    Parks, J. Robert; Plavchan, Peter; Gee, Alan H. [Infrared Processing and Analysis Center, California Institute of Technology, Mail Code 100-22, 770 South Wilson Avenue, Pasadena, CA 91125 (United States); White, Russel J., E-mail: parksj@chara.gsu.edu [Georgia State University, Department of Physics and Astronomy, 25 Park Place, Room 605, Atlanta, GA 30303 (United States)

    2014-03-01

    Presented are the results of a near-IR photometric survey of 1678 stars in the direction of the ρ Ophiuchus (ρ Oph) star forming region using data from the 2MASS Calibration Database. For each target in this sample, up to 1584 individual J-, H-, and K{sub s} -band photometric measurements with a cadence of ∼1 day are obtained over three observing seasons spanning ∼2.5 yr; it is the most intensive survey of stars in this region to date. This survey identifies 101 variable stars with ΔK{sub s} -band amplitudes from 0.044 to 2.31 mag and Δ(J – K{sub s} ) color amplitudes ranging from 0.053 to 1.47 mag. Of the 72 young ρ Oph star cluster members included in this survey, 79% are variable; in addition, 22 variable stars are identified as candidate members. Based on the temporal behavior of the K{sub s} time-series, the variability is distinguished as either periodic, long time-scale or irregular. This temporal behavior coupled with the behavior of stellar colors is used to assign a dominant variability mechanism. A new period-searching algorithm finds periodic signals in 32 variable stars with periods between 0.49 to 92 days. The chief mechanism driving the periodic variability for 18 stars is rotational modulation of cool starspots while 3 periodically vary due to accretion-induced hot spots. The time-series for six variable stars contains discrete periodic ''eclipse-like'' features with periods ranging from 3 to 8 days. These features may be asymmetries in the circumstellar disk, potentially sustained or driven by a proto-planet at or near the co-rotation radius. Aperiodic, long time-scale variations in stellar flux are identified in the time-series for 31 variable stars with time-scales ranging from 64 to 790 days. The chief mechanism driving long time-scale variability is variable extinction or mass accretion rates. The majority of the variable stars (40) exhibit sporadic, aperiodic variability over no discernable time-scale. No chief

  2. Radiation-disorder and aperiodicity in irradiated ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Hobbs, L.W.

    1992-01-01

    This final technical report documents the accomplishments of the program of research entitled Radiation Disorder and Aperiodicity in Irradiated Ceramics'' for the period June 22, 1989--June 21, 1992. This research forms the latest part on an on-going program, begun at MIT in 1983 under DOE support, which has had as its objectives investigation of the responses in radiation environments of ceramics heavily-irradiated with electrons, neutrons and ions, with potential applications to fusion energy technology and high-level nuclear waste storage. Materials investigated have included SiO{sub 2}, MgAl{sub 2}O{sub 4}, Al{sub 23}O{sub 27}N{sub 5}, SiC, BeO, LiAlO{sub 2}, Li{sub 2}ZrO{sub 3}, CaTiO{sub 3}KTaO{sub 3} and Ca(Zr, Pu)Ti{sub 2}O{sub 7}. The program initially proposed for 1989 had as its major objectives two main thrusts: (1) research on defect aggregation in irradiated non-oxide ceramics, and (2) research on irradiation-induced amorphization of network silicas and phosphates.

  3. Consensus of Multiagent Systems Using Aperiodic Sampled-Data Control.

    Science.gov (United States)

    Wu, Yuanqing; Su, Hongye; Shi, Peng; Shu, Zhan; Wu, Zheng-Guang

    2016-09-01

    This paper is concerned with the consensus of multiagent systems with nonlinear dynamics through the use of aperiodic sampled-data controllers, which are more flexible than classical periodic sampled-data controllers. By input delay approach, the resulting sampled-data system is reformulated as a continuous system with time-varying delay in the control input. A continuous Lyapunov functional, which captures the information on sampling pattern, together with the free-weighting matrix method, is then used to establish a sufficient condition for consensusability. For a more general case that the sampled-data controllers are subject to constant input delays, a novel discontinuous Lyapunov functional is introduced on the basis of the vector extension of Wirtinger's inequality. This functional can lead to simplified and efficient stability conditions for computation and optimization. Further results on the estimate of maximal allowable sampling interval upper bound is given as well. Numerical example is provided to show the effectiveness and merits of the proposed protocol.

  4. Reclaiming Spare Capacity and Improving Aperiodic Response Times in Real-Time Environments

    Directory of Open Access Journals (Sweden)

    Liu Xue

    2011-01-01

    Full Text Available Abstract Scheduling recurring task sets that allow some instances of the tasks to be skipped produces holes in the schedule which are nonuniformly distributed. Similarly, when the recurring tasks are not strictly periodic but are sporadic, there is extra processor bandwidth arising because of irregular job arrivals. The additional computation capacity that results from skips or sporadic tasks can be reclaimed to service aperiodic task requests efficiently and quickly. We present techniques for improving the response times of aperiodic tasks by identifying nonuniformly distributed spare capacity—because of skips or sporadic tasks—in the schedule and adding such extra capacity to the capacity queue of a BASH server. These gaps can account for a significant portion of aperiodic capacity, and their reclamation results in considerable improvement to aperiodic response times. We present two schemes: NCLB-CBS, which performs well in periodic real-time environments with firm tasks, and NCLB-CUS, which can be deployed when the basic task set to schedule is sporadic. Evaluation via simulations and implementation suggests that performance improvements for aperiodic tasks can be obtained with limited additional overhead.

  5. A study of periodic and aperiodic ferromagnetic antidot lattices

    Science.gov (United States)

    Bhat, Vinayak S.

    This thesis reports our study of the effect of domain wall pinning by ferromagnetic (FM) metamaterials [1] in the form of periodic antidot lattices (ADL) on spin wave spectra in the reversible regime. This study was then extended to artificial quasicrystals in the form of Penrose P2 tilings (P2T). Our DC magnetization study of these metamaterials showed reproducible and temperature dependent knee anomalies in the hysteretic regime that are due to the isolated switching of the FM segments. Our dumbbell model analysis [2] of simulated magnetization maps indicates that FM switching in P2T is nonstochastic . We have also acquired the first direct, two-dimensional images of the magnetization of Permalloy films patterned into P2T using scanning electron microscopy with polarization analysis (SEMPA). Our SEMPA images demonstrate P2T behave as geometrically frustrated networks of narrow ferromagnetic film segments having near-uniform, bipolar (Ising-like) magnetization, similar to artificial spin ices (ASI). We find the unique aperiodic translational symmetry and diverse vertex coordination of multiply-connected P2T induce a more complex spin-ice behavior driven by exchange interactions in vertex domain walls, which differs markedly from the behavior of disconnected ASI governed only by dipolar interactions. Keywords: Ferromagnetic Antidot Lattices, Metamaterials, Ferromagnetic Resonance, Artificial Quasicrystal, Artificial Spin Ice. [1] VV Kruglyak et al. "Magnonic metamaterials". In: Metamaterial, edited by X.-Y. Jiang (InTech, 2012) (2012). [2] Claudio Castelnovo, Roderich Moessner, and Shivaji L Sondhi. "Magnetic monopoles in spin ice". In: Nature 451.7174 (2008), pp. 42--45.

  6. Deterministic aperiodic composite lattice-structured silicon thin films for photon management

    CERN Document Server

    Xavier, Jolly; Becker, Christiane

    2016-01-01

    Exotic manipulation of the flow of photons in nanoengineered semiconductor materials with an aperiodic distribution of nanostructures plays a key role in efficiency-enhanced and industrially viable broadband photonic technologies. Through a generic deterministic nanotechnological route, in addition to periodic, transversely quasicrystallographic or disordered random photonic lattices, here we show scalable nanostructured semiconductor thin films on large area nanoimprinted substrates up to 4cm^2 with advanced functional features of aperiodic composite nanophotonic lattices having tailorable supercell tiles. The richer Fourier spectra of the presented artificially nanostructured materials with well-defined lattice point morphologies are designed functionally akin to two-dimensional incommensurate intergrowth aperiodic lattices-comprising periodic photonic crystals and in-plane quasicrystals as subgroups. The composite photonic lattice-structured crystalline silicon thin films with tapered nanoholes or nanocone...

  7. Structural color of a lycaenid butterfly: analysis of an aperiodic multilayer structure.

    Science.gov (United States)

    Yoshioka, S; Shimizu, Y; Kinoshita, S; Matsuhana, B

    2013-12-01

    We investigated the structural color of the green wing of the lycaenid butterfly Chrysozephyrus brillantinus. Electron microscopy revealed that the bottom plate of the cover scale on the wing consists of an alternating air-cuticle multilayer structure. However, the thicknesses of the layers were not constant but greatly differed depending on the layer, unlike the periodic multilayer designs often adopted for artificial laser-reflecting mirrors. The agreement between the experimentally determined and theoretically calculated reflectance spectra led us to conclude that the multilayer interference in the aperiodic system is the primary origin of the structural color. We analyzed optical interference in this aperiodic system using a simple analytical model and found that two spectral peaks arise from constructive interference among different parts of the multilayer structure. We discuss the advantages and disadvantages of the aperiodic system over a periodic one.

  8. The structure model of a cubic aperiodic phase ('quasicrystal without forbidden symmetry axes').

    Science.gov (United States)

    Kraposhin, V S; Talis, A L; Thanh Lam, Ha

    2008-03-19

    A model structure of the aperiodic cubic phase (a cubic quasicrystal) has been constructed as a periodical packing of hierarchical octahedral clusters which were composed of truncated tetrahedra (Friauf-Laves polyhedra) and chains of Frank-Kasper polyhedra with 14 vertices. The construction of the hierarchical model for the cubic aperiodic phase became possible due to the discovery of a new space subdivision with equal edges and with vertices belonging to two orbits of the space group Fm3m. The subdivision is characterized by unique values and unique relations between the coordinates of the starting points of two orbits. Calculated x-ray diffraction patterns for the proposed hierarchical model are in qualitative agreement with published experimental x-ray patterns for aperiodical phases observed in melt-quenched Mg-Al and Fe-Nb-B-Si alloys.

  9. Co-universal C*-algebras associated to aperiodic k-graphs

    OpenAIRE

    Kang, Sooran; Sims, Aidan

    2011-01-01

    We construct a representation of each finitely aligned aperiodic k-graph \\Lambda\\ on the Hilbert space H^{ap} with basis indexed by aperiodic boundary paths in \\Lambda. We show that the canonical expectation on B(H^{ap}) restricts to an expectation of the image of this representation onto the subalgebra spanned by the final projections of the generating partial isometries. We then show that every quotient of the Toeplitz algebra of the k-graph admits an expectation compatible with this one. U...

  10. Optimized aperiodic broadband thermal emitters for use as light bulb filaments

    CERN Document Server

    Granier, Christopher H; Veronis, Georgios; Dowling, Jonathan P

    2016-01-01

    We present optimized aperiodic structures for use as broadband thermal incandescent emitters which are capable of increasing the emittance by nearly a factor of two over the visible wavelength range when compared to bulk tungsten. These aperiodic multilayer structures are designed with alternating layers of tungsten and air or tungsten and silicon carbide on top of a tungsten substrate. We investigate the properties of these structures for use as lightbulb filaments. We find that these structures greatly enhance the emittance over the visible wavelength range, while also increasing the overall efficiency of the bulb and could lead to a decrease in incandescent lightbulb power consumption by nearly 50%.

  11. Extended field-of-view in a lensless endoscope using an aperiodic multicore fiber

    CERN Document Server

    Sivankutty, Siddharth; Bouwmans, Géraud; Kogan, Dani; Oron, Dan; Andresen, Esben Ravn; Rigneault, Hervé

    2016-01-01

    We investigate lensless endoscopy using coherent beam combining and aperiodic multicore fibers (MCF). We show that diffracted orders, inherent to MCF with periodically arranged cores, dramatically reduce the field of view (FoV) and that randomness in MCF core positions can increase the FoV up to the diffraction limit set by a single fiber core, while maintaining MCF experimental feasibility. We demonstrate experimentally pixelation-free lensless endoscopy imaging over a 120 micron FoV with an aperiodic MCF designed with widely spaced cores. We show that this system is suitable to perform beam scanning imaging by simply applying a tilt to the proximal wavefront.

  12. An aperiodic phenomenon of the unscented Kalman filter in filtering noisy chaotic signals

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A non-periodic oscillatory behavior of the unscented Kalman filter (UKF) when used to filter noisy contaminated chaotic signals is reported. We show both theoretically and experimentally that the gain of the UKF may not converge or diverge but oscillate aperiodically. More precisely, when a nonlinear system is periodic, the Kalman gain and error covariance of the UKF converge to zero. However, when the system being considered is chaotic, the Kalman gain either converges to a fixed point with a magnitude larger than zero or oscillates aperiodically.

  13. Synchronization of neural networks with stochastic perturbation via aperiodically intermittent control.

    Science.gov (United States)

    Zhang, Wei; Li, Chuandong; Huang, Tingwen; Xiao, Mingqing

    2015-11-01

    In this paper, the synchronization problem for neural networks with stochastic perturbation is studied with intermittent control via adaptive aperiodicity. Under the framework of stochastic theory and Lyapunov stability method, we develop some techniques of intermittent control with adaptive aperiodicity to achieve the synchronization of a class of neural networks, modeled by stochastic systems. Some effective sufficient conditions are established for the realization of synchronization of the underlying network. Numerical simulations of two examples are provided to illustrate the theoretical results obtained in the paper.

  14. Electronic spectrum and localization of electronic states in aperiodic quantum dot chains

    Science.gov (United States)

    Korotaev, P. Yu.; Vekilov, Yu. Kh.; Kaputkina, N. E.

    2014-02-01

    The electronic energy spectra of aperiodic Thue-Morse, Rudin-Shapiro, and double-periodic quantum dot chains are investigated in the tight-binding approximation. The dependence of the spectrum on all parameters of a "mixed" aperiodic chain model is studied: the electronic energy at quantum dots and the hopping integrals. The electronic degree of localization in the chains under consideration is determined by analyzing the inverse participation ratio. Its spectral distribution and the dependence of the band-averaged degree of localization on these model parameters have been calculated. It is shown that a transition of the system's sites to a resonant state in which the degree of electron localization decreases, while an overlap between the subbands occurs in the spectrum is possible when the parameters are varied.

  15. Aperiodic signals processing via parameter-tuning stochastic resonance in a photorefractive ring cavity

    Directory of Open Access Journals (Sweden)

    Xuefeng Li

    2014-04-01

    Full Text Available Based on solving numerically the generalized nonlinear Langevin equation describing the nonlinear dynamics of stochastic resonance by Fourth-order Runge-Kutta method, an aperiodic stochastic resonance based on an optical bistable system is numerically investigated. The numerical results show that a parameter-tuning stochastic resonance system can be realized by choosing the appropriate optical bistable parameters, which performs well in reconstructing aperiodic signals from a very high level of noise background. The influences of optical bistable parameters on the stochastic resonance effect are numerically analyzed via cross-correlation, and a maximum cross-correlation gain of 8 is obtained by optimizing optical bistable parameters. This provides a prospective method for reconstructing noise-hidden weak signals in all-optical signal processing systems.

  16. Remarks on disorder and aperiodicity in a model for interacting polymers

    Science.gov (United States)

    Haddad, T. A. S.; Andrade, R. F. S.; Salinas, S. R.

    2004-12-01

    We present a comparative study of the effects of random and aperiodically distributed interactions on the critical behavior of a model for two interacting polymers on a diamond hierarchical lattice. The problem is formulated in terms of exact renormalization-group (RG) recursion relations. In the disordered case, it is possible to develop a perturbative treatment in order to obtain the fixed points of the moments associated with the random distribution of interactions. Fully uncorrelated disorder may become relevant, driving the system away from a homogeneous fixed point. Layered disorder may lead to a breakdown of the perturbative treatment. In the case of aperiodic interactions, we also show some examples of relevance and irrelevance of geometric fluctuations, and further investigate the models by resorting to an independent transfer-matrix (TM) analysis, which fully corroborates the scaling results.

  17. Aperiodic signals processing via parameter-tuning stochastic resonance in a photorefractive ring cavity

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xuefeng, E-mail: lixfpost@163.com [School of Science, Xi' an University of Post and Telecommunications, Xi' an, 710121 (China); Cao, Guangzhan; Liu, Hongjun [Xi' an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi' an, 710119 (China)

    2014-04-15

    Based on solving numerically the generalized nonlinear Langevin equation describing the nonlinear dynamics of stochastic resonance by Fourth-order Runge-Kutta method, an aperiodic stochastic resonance based on an optical bistable system is numerically investigated. The numerical results show that a parameter-tuning stochastic resonance system can be realized by choosing the appropriate optical bistable parameters, which performs well in reconstructing aperiodic signals from a very high level of noise background. The influences of optical bistable parameters on the stochastic resonance effect are numerically analyzed via cross-correlation, and a maximum cross-correlation gain of 8 is obtained by optimizing optical bistable parameters. This provides a prospective method for reconstructing noise-hidden weak signals in all-optical signal processing systems.

  18. Photonic band structure of one-dimensional aperiodic superlattices composed of negative refraction metamaterials

    Science.gov (United States)

    Tyc, Michał H.; Salejda, Włodzimierz; Klauzer-Kruszyna, Agnieszka; Tarnowski, Karol

    2007-05-01

    The dispersion relation for polarized light transmitting through a one-dimensional superlattice composed of aperiodically arranged layers made of ordinary dielectric and negative refraction metamaterials is calculated with finite element method. Generalized Fibonacci, generalized Thue-Morse, double-periodic and Rudin-Shapiro superlattices are investigated, using their periodic approximants. Strong dispersion of metamaterials is taken into account. Group velocities and effective refraction indices in the structures are calculated. The self-similar structure of the transmission spectra is observed.

  19. Optimized Second Harmonic Generation of Femtosecond Pulse by Phase-Blanking Effect in Aperiodically Optical Superlattice

    Institute of Scientific and Technical Information of China (English)

    KONG Yan; CHEN Xian-Feng; XIA Yu-Xing

    2008-01-01

    @@ In order to minimize the effect of the unconsidered frequency components on the generated compression pulse,the phasing-blanking effect is taken into account of designing the one-dimensional aperiodic domain reversal structure. Hierarchic genetic algorithm for the design of a domain reversal grating to modulate the spectrum and phase of the generated SH pulse simultaneously are presented. Our simulation shows that the quality of an output pulse is fairly improved.

  20. Aperiodicity in one-way Markov cycles and repeat times of large earthquakes in faults

    CERN Document Server

    Tejedor, Alejandro; Pacheco, Amalio F

    2011-01-01

    A common use of Markov Chains is the simulation of the seismic cycle in a fault, i.e. as a renewal model for the repetition of its characteristic earthquakes. This representation is consistent with Reid's elastic rebound theory. Here it is proved that in {\\it any} one-way Markov cycle, the aperiodicity of the corresponding distribution of cycle lengths is always lower than one. This fact concurs with observations of large earthquakes in faults all over the world.

  1. Real-time remedial action against aperiodic small signal rotor angle instability

    DEFF Research Database (Denmark)

    Weckesser, Johannes Tilman Gabriel; Jóhannsson, Hjörtur; Østergaard, Jacob

    2016-01-01

    This paper presents a method that in real-time determines remedial actions, which restore stable operation with respect to aperiodic small signal rotor angle stability (ASSRAS) when insecure or unstable operation has been detected. An ASSRAS assessment method is used to monitor the stability boun...... on the IEEE 14-bus and the Nordic32 test systems where results show that the method can efficiently determine the required active power redispatch to avoid an imminent instability....

  2. Break of universality for an Ising model with aperiodic Rudin-Shapiro interactions

    Science.gov (United States)

    Andrade, R. F. S.; Pinho, S. T. R.

    2003-08-01

    We analyze the ferromagnetic Ising model on non-Euclidean scale invariant lattices with aperiodic interactions ( J A , J B , J C , J D ) defined by Rudin-Shapiro substitution rules with Migdal-Kadanoff renormalization (MKR) and transfer matrix (TM) techniques. The analysis of the invariant sets of the zero-field MKR transformation indicates that the critical behavior, completely distinct from the one of the uniform model, is described by a new off-diagonal fixed point. This contrasts with other aperiodic models where the new critical behavior is described by a period-two cycle. With the new fixed point, values for the thermal critical exponents, α and ν, as well as the period of log-periodic oscillations, are obtained. Exact recursive maps for all thermodynamical functions are derived within the TM approach. The explicit dependence of the thermodynamical functions with respect to temperature is evaluated by the numerical iteration of the set of maps until a previously chosen convergence is achieved. They also indicate that, depending on the actual choice for the aperiodic coupling constants, the magnetic exponents (β and γ) assume different values. However the Rushbrook relation is always satisfied.

  3. Review Article: "The Lagrangian description of aperiodic flows: a case study of the Kuroshio Current"

    Directory of Open Access Journals (Sweden)

    C. Mendoza

    2012-08-01

    Full Text Available This article reviews several recently developed Lagrangian tools and shows how their combined use succeeds in obtaining a detailed description of purely advective transport events in general aperiodic flows. In particular, because of the climate impact of ocean transport processes, we illustrate a 2-D application on altimeter data sets over the area of the Kuroshio Current, although the proposed techniques are general and applicable to arbitrary time dependent aperiodic flows. The first challenge for describing transport in aperiodical time dependent flows is obtaining a representation of the phase portrait where the most relevant dynamical features may be identified. areas that are related to confinement regions. This representation is accomplished by using global Lagrangian descriptors that when applied for instance to the altimeter data sets retrieve over the ocean surface a phase portrait where the geometry of interconnected dynamical systems is visible. The phase portrait picture is essential because it evinces which transport routes are acting on the whole flow. Once these routes are roughly recognised, it is possible to complete a detailed description by the direct computation of the finite time stable and unstable manifolds of special hyperbolic trajectories that act as organising centres of the flow.

  4. Maximizing the bandwidth of coherent, mid-IR supercontinuum using highly nonlinear aperiodic nanofibers

    Science.gov (United States)

    Baili, Amira; Cherif, Rim; Heidt, Alexander; Zghal, Mourad

    2014-05-01

    We describe in detail a new procedure of maximizing the bandwidth of mid-infrared (mid-IR) supercontinuum (SC) in highly nonlinear microstructured As2Se3 and tellurite aperiodic nanofibers. By introducing aperiodic rings of first and secondary air holes into the cross-sections of our microstructured fiber designs, we achieve flattened and all-normal dispersion profiles over much broader bandwidths than would be possible with simple periodic designs. These fiber designs are optimized for efficient, broadband, and coherent SC generation in the mid-IR spectral region. Numerical simulations show that these designs enable the generation of a SC spanning over 2290 nm extending from 1140 to 3430 nm in 8 cm length of tellurite nanofiber with input energy of E = 200 pJ and a SC bandwidth of over 4700 nm extending from 1795 to 6525 nm generated in only 8 mm-length of As2Se3-based nanofiber with input energy as low as E = 100 pJ. This work provides a new type of broadband mid-IR SC source with flat spectral shape as well as excellent coherence and temporal properties by using aperiodic nanofibers with all-normal dispersion suitable for applications in ultrafast science, metrology, coherent control, non-destructive testing, spectroscopy, and optical coherence tomography in the mid-IR region.

  5. Simulation methods for multiperiodic and aperiodic nanostructured dielectric waveguides

    DEFF Research Database (Denmark)

    Paulsen, Moritz; Neustock, Lars Thorben; Jahns, Sabrina

    2017-01-01

    on Rudin–Shapiro, Fibonacci, and Thue–Morse binary sequences. The near-field and far-field properties are computed employing the finite-element method (FEM), the finite-difference time-domain (FDTD) method as well as a rigorous coupled wave algorithm (RCWA). The results show that all three methods...

  6. Simulation of photonic waveguides with deterministic aperiodic nanostructures for biosensing

    DEFF Research Database (Denmark)

    Neustock, Lars Thorben; Paulsen, Moritz; Jahns, Sabrina

    2016-01-01

    -field and far-field properties of structures based on a Rudin-Shapiro binary sequence. All simulation methods predict multiple resonances with sensitivities in the range of 30 nm/RIU to 60 nm/RIU for bulk refractive index measurements. Local functionalization is estimated to improve the sensitivity...

  7. Simulation Methods for Multiperiodic and Aperiodic Nanostructured Dielectric Waveguides

    DEFF Research Database (Denmark)

    Paulsen, Moritz; Neustock, Lars Thorben; Jahns, Sabrina

    on Rudin-Shapiro, Fibonacci, and Thue-Morse binary sequences. The near-field and far-field properties are calculated employing the finite-element method (FEM), the finite- difference time-domain (FDTD) method as well as a rigorous coupled wave algorithm (RCWA). References [1] S. V. Boriskina, A. Gopinath...

  8. Simulation of photonic waveguides with deterministic aperiodic nanostructures for biosensing

    DEFF Research Database (Denmark)

    Neustock, Lars Thorben; Paulsen, Moritz; Jahns, Sabrina;

    -field and far-field properties of structures based on a Rudin-Shapiro binary sequence. All simulation methods predict multiple resonances with sensitivities in the range of 30 nm/RIU to 60 nm/RIU for bulk refractive index measurements. Local functionalization is estimated to improve the sensitivity...

  9. Aperiodic structures and notions of order and disorder

    Science.gov (United States)

    Ben-Abraham, S. I.; Quandt, A.

    2011-07-01

    The fabrication of artificial heterostructures is mainly based on substitution systems. We present simple ways to construct double-sided versions of the Fibonacci, Prouhet-Thue-Morse, paperfolding, period doubling and Golay-Rudin-Shapiro sequences. We also construct a generic instance of the two-dimensional Prouhet-Thue-Morse structure and explore its symbolic complexity. The complexity turns out to be polynomial and hence, the entropy goes to zero.

  10. External Description for Multivariable Systems Sampled in an Aperiodic Way

    CERN Document Server

    Fúster-Sabater, Amparo

    2010-01-01

    An external description for nonperiodically sampled multivariable linear systems has been developed. Emphasis is on the sampling period sequence, included among the variables to be handled. The computational procedure is simple and no use of polynomial matrix theory is required. This input/output description is believed to be a basic formulation for its later application to the problem of optimal control and/or identification of linear dynamical systems.

  11. Structural parameters and their effects on the electronic transport properties in aperiodic superlattice profile

    Science.gov (United States)

    Bendahma, F.; Djelti, R.; Bentata, S.

    2016-08-01

    The aperiodic GaAs/AlxGa1-xAs superlattices (SL) with trimer disorder have been studied in this paper. The transfer-matrix technique and the exact Airy function formalism have been used to determine the miniband structure, the transmission coefficient, the resonance energy and resonant tunneling time (RTT). Although the disorder localizes the states on average, our numerical calculations show that the localization length of the states becomes more extended when the disorder is correlated (trimer case). We have also found that the RTT is of the order of several femtoseconds.

  12. INVERSE CORRECTION OF FOURIER TRANSFORMS FOR ONE-DIMENSIONAL STRONGLY SCATTERING APERIODIC LATTICES

    Directory of Open Access Journals (Sweden)

    Y. F. Hsin

    2016-05-01

    Full Text Available The accuracy of the Fourier transform (FT, advantageous for the aperiodic lattice (AL design, is significantly improved for strongly scattering periodic lattices (PLs and ALs. The approach is to inversely obtain corrected parameters from an accurate transfer matrix method for the FT. We establish a corrected FT in order to improve the spectral inaccuracy of strongly scattering PLs by redefining wave numbers and reflective intensity. We further correct the FT for strongly scattering ALs by implementing improvements applied to strongly scattering PLs and then making detailed wave number adjustments in the main band spectral region. Silicon lattice simulations are presented.

  13. Scaling in the Optical Characteristics of Aperiodic Structures with Self-Similarity Symmetry

    Energy Technology Data Exchange (ETDEWEB)

    Zotov, A. M.; Korolenko, P. V., E-mail: pvkorolenko@rambler.ru; Mishin, A. Yu. [Moscow State University (Russian Federation)

    2010-11-15

    The properties of diffraction gratings and multilayered systems constructed using 1D models of quasicrystals are considered based on numerical simulation. It is shown that there is a direct relationship between the self-similarity symmetry of quasicrystals and scaling in the characteristics of the above-mentioned optical devices. The degree of structural correspondence between the graphical representations of the geometric properties of crystals, light diffraction patterns of gratings, and the transmission spectra of multilayered systems is estimated. It is shown that certain types of self-similarity symmetry make the characteristics of aperiodic diffraction gratings highly stable to a change in the size ratio of forming elements.

  14. Wide-Area Assessment of Aperiodic Small Signal Rotor Angle Stability in Real-Time

    DEFF Research Database (Denmark)

    Jóhannsson, Hjörtur; Nielsen, Arne Hejde; Østergaard, Jacob

    2013-01-01

    This paper presents the details of a new real-time stability assessment method. The method assesses a particular mechanism of stability: each generator’s capability to generate sufficient steady state electromechanical torque. The lack of sufficient steady state torque causes aperiodic increase...... of multiple operating points is derived in the paper. Finally, results from time-domain simulation of instability scenarios in the Nordic32 test system are presented and results used for testing the assessment method. The results illustrate the method’s capability to efficiently identify the location...

  15. Wide-Area Assessment of Aperiodic Small Signal Rotor Angle Stability in Real-Time

    DEFF Research Database (Denmark)

    Jóhannsson, Hjörtur; Nielsen, Arne Hejde; Østergaard, Jacob

    2014-01-01

    This paper presents the details of a new real-time stability assessment method. The method assesses a particular mechanism of stability: each generator's capability to generate sufficient steady state electromechanical torque. The lack of sufficient steady state torque causes aperiodic increase...... of multiple operating points is derived in the paper. Finally, results from timedomain simulation of instability scenarios in the Nordic32 test system are presented and results used for testing the assessment method. The results illustrate the method's capability to efficiently identify the location...

  16. Periodic and aperiodic traveling pulses in population dynamics: An example from the occurrence of epidemic infections

    Science.gov (United States)

    Vecchio, A.; Primavera, L.; Carbone, V.

    2006-03-01

    The dynamics of the occurrence of the dengue hemorrhagic fever in the 72 provinces of Thailand is investigated by performing a proper orthogonal decomposition (POD) on spatiotemporal data. Using this technique, we are able to identify and select the contribution of different modes, selected according to the energy content, to the evolution of the epidemic during 14 years. We found that the phenomenon is characterized by periodic cycles of yearly occurrence characterized by spatial scales of about 420 km. Superimposed on this basic mode, POD analysis is able to reveal the presence of high-energetic aperiodic traveling pulses of the epidemic, which extend spatially for about 510 km from Bangkok.

  17. Optimized emission in nanorod arrays through quasi-aperiodic inverse design.

    Science.gov (United States)

    Anderson, P Duke; Povinelli, Michelle L

    2015-06-01

    We investigate a new class of quasi-aperiodic nanorod structures for the enhancement of incoherent light emission. We identify one optimized structure using an inverse design algorithm and the finite-difference time-domain method. We carry out emission calculations on both the optimized structure as well as a simple periodic array. The optimized structure achieves nearly perfect light extraction while maintaining a high spontaneous emission rate. Overall, the optimized structure can achieve a 20%-42% increase in external quantum efficiency relative to a simple periodic design, depending on material quality.

  18. Bloch-like surface waves in Fibonacci quasi-crystals and Thue-Morse aperiodic dielectric multilayers

    Science.gov (United States)

    Koju, Vijay; Robertson, William M.

    2016-09-01

    Bloch surface waves (BSWs) in periodic dielectric multilayer structures with surface defect have been extensively studied. However, it has recently been recognized that quasi-crystals and aperiodic dielectric multilayers also support Bloch-like surface waves (BLSWs). In this work, we numerically show the existence of BLSWs in Fibonacci quasi-crystals and Thue-Morse aperiodic dielectric multilayers using the prism coupling technique. We compare the surface field enhancement and penetration depth of BLSWs in these structures with that of BSWs in their periodic counterparts.

  19. Aperiodic linear networked control considering variable channel delays: application to robots coordination.

    Science.gov (United States)

    Santos, Carlos; Espinosa, Felipe; Santiso, Enrique; Mazo, Manuel

    2015-05-27

    One of the main challenges in wireless cyber-physical systems is to reduce the load of the communication channel while preserving the control performance. In this way, communication resources are liberated for other applications sharing the channel bandwidth. The main contribution of this work is the design of a remote control solution based on an aperiodic and adaptive triggering mechanism considering the current network delay of multiple robotics units. Working with the actual network delay instead of the maximum one leads to abandoning this conservative assumption, since the triggering condition is fixed depending on the current state of the network. This way, the controller manages the usage of the wireless channel in order to reduce the channel delay and to improve the availability of the communication resources. The communication standard under study is the widespread IEEE 802.11g, whose channel delay is clearly uncertain. First, the adaptive self-triggered control is validated through the TrueTime simulation tool configured for the mentioned WiFi standard. Implementation results applying the aperiodic linear control laws on four P3-DX robots are also included. Both of them demonstrate the advantage of this solution in terms of network accessing and control performance with respect to periodic and non-adaptive self-triggered alternatives.

  20. Aperiodic Linear Networked Control Considering Variable Channel Delays: Application to Robots Coordination

    Directory of Open Access Journals (Sweden)

    Carlos Santos

    2015-05-01

    Full Text Available One of the main challenges in wireless cyber-physical systems is to reduce the load of the communication channel while preserving the control performance. In this way, communication resources are liberated for other applications sharing the channel bandwidth. The main contribution of this work is the design of a remote control solution based on an aperiodic and adaptive triggering mechanism considering the current network delay of multiple robotics units. Working with the actual network delay instead of the maximum one leads to abandoning this conservative assumption, since the triggering condition is fixed depending on the current state of the network. This way, the controller manages the usage of the wireless channel in order to reduce the channel delay and to improve the availability of the communication resources. The communication standard under study is the widespread IEEE 802.11g, whose channel delay is clearly uncertain. First, the adaptive self-triggered control is validated through the TrueTime simulation tool configured for the mentioned WiFi standard. Implementation results applying the aperiodic linear control laws on four P3-DX robots are also included. Both of them demonstrate the advantage of this solution in terms of network accessing and control performance with respect to periodic and non-adaptive self-triggered alternatives.

  1. Gate-controlled mid-infrared light bending with aperiodic graphene nanoribbons array

    CERN Document Server

    Carrasco, Eduardo; Mosig, Juan R; Low, Tony; Perruisseau-Carrier, Julien

    2014-01-01

    Graphene plasmonic nanostructures enable subwavelength confinement of electromagnetic energy from the mid-infrared down to the terahertz frequencies. By exploiting the spectrally varying light scattering phase at vicinity of the resonant frequency of the plasmonic nanostructure, it is possible to control the angle of reflection of an incoming light beam. We demonstrate, through full-wave electromagnetic simulations based on Maxwell equations, the electrical control of the angle of reflection of a mid-infrared light beam by using an aperiodic array of graphene nanoribbons, whose widths are engineered to produce a spatially varying reflection phase profile that allows for the construction of a far-field collimated beam towards a predefined direction.

  2. The instability condition of the aperiodic ordinary mode for new scalings of the counterstreaming parameters

    Energy Technology Data Exchange (ETDEWEB)

    Vafin, S.; Schlickeiser, R. [Institut für Theoretische Physik, Lehrstuhl IV: Weltraum- and Astrophysik, Ruhr-Universität, Bochum (Germany); Lazar, M. [Institut für Theoretische Physik, Lehrstuhl IV: Weltraum- and Astrophysik, Ruhr-Universität, Bochum (Germany); Center for Plasma Astrophysics, Celestijnenlaan 200 B, 3001 Leuven (Belgium)

    2015-02-15

    The aperiodic ordinary (O-) mode instability in homogeneous and collisionless plasmas with kinetic anisotropies has recently received renewed attention due to its potential application in the solar wind, as well as for equal-mass plasmas. The present paper revisits the marginal instability condition of the O-mode derived from the electromagnetic linear dispersion equation for waves propagating perpendicular to the background magnetic field. For a counterstreaming bi-Maxwellian plasma system, this condition is found to be significantly affected by the streaming parameters. New functional dependencies (not studied before) of the counterstreaming parameters on the magnetic field and the other plasma parameters lead to new conditions of this instability for the both equal mass and electron-proton plasmas.

  3. The Time Is Up: Compression of Visual Time Interval Estimations of Bimodal Aperiodic Patterns

    Directory of Open Access Journals (Sweden)

    Fabiola Duarte

    2017-08-01

    Full Text Available The ability to estimate time intervals subserves many of our behaviors and perceptual experiences. However, it is not clear how aperiodic (AP stimuli affect our perception of time intervals across sensory modalities. To address this question, we evaluated the human capacity to discriminate between two acoustic (A, visual (V or audiovisual (AV time intervals of trains of scattered pulses. We first measured the periodicity of those stimuli and then sought for correlations with the accuracy and reaction times (RTs of the subjects. We found that, for all time intervals tested in our experiment, the visual system consistently perceived AP stimuli as being shorter than the periodic (P ones. In contrast, such a compression phenomenon was not apparent during auditory trials. Our conclusions are: first, the subjects exposed to P stimuli are more likely to measure their durations accurately. Second, perceptual time compression occurs for AP visual stimuli. Lastly, AV discriminations are determined by A dominance rather than by AV enhancement.

  4. Short term aperiodic variability of X-ray binaries: its origin and implications

    CERN Document Server

    Revnivtsev, M

    2008-01-01

    In this review I briefly describe the latest advances in studies of aperiodic variability of accreting X-ray binaries and outline the model which currently describe the majority of observational appearances of variability of accreting sources in the best way. Then I concentrate on the case of luminous accreting neutron star binaries (in the soft/high spectral state), where study of variability of X-ray emission of sources allowed us to resolve long standing problem of disentangling the contribution of accretion disk and boundary/spreading layer components to the time average spectrum of sources. The obtained knowledge of the shape of the spectrum of the boundary layer allowed us to make estimates of the mass and radii of accreting neutron stars.

  5. Wide Area Prosumption Control and Sensitivities of Aperiodic Small Signal Stability Indicators

    DEFF Research Database (Denmark)

    Wittrock, Martin Lindholm; Jóhannsson, Hjörtur; Nielsen, Arne Hejde

    2014-01-01

    and patterns, stability indicators for aperiodic small signal angular stability (ASSA) are examined, while the concept of prosumption is described. The methodology presented is shown to be able to assess the margin to instability and to predict how this margin can be affected if a load is changed in the grid......This paper introduces the concept of prosumption control where intelligent loads and distributed generation are aggregated and controlled to improve power system security. It is expected that intelligent load and generation units can respond to control / market signals and thus present...... an opportunity of available resources for changing the operating point (OP) of a system to one that is more secure. A prosumption pattern is then a signal to prosumers to shift their demand in time. This makes it possible to temporarily change the distribution of the power demand. A prosumption pattern...

  6. Applied optics. Gain modulation by graphene plasmons in aperiodic lattice lasers.

    Science.gov (United States)

    Chakraborty, S; Marshall, O P; Folland, T G; Kim, Y-J; Grigorenko, A N; Novoselov, K S

    2016-01-15

    Two-dimensional graphene plasmon-based technologies will enable the development of fast, compact, and inexpensive active photonic elements because, unlike plasmons in other materials, graphene plasmons can be tuned via the doping level. Such tuning is harnessed within terahertz quantum cascade lasers to reversibly alter their emission. This is achieved in two key steps: first, by exciting graphene plasmons within an aperiodic lattice laser and, second, by engineering photon lifetimes, linking graphene's Fermi energy with the round-trip gain. Modal gain and hence laser spectra are highly sensitive to the doping of an integrated, electrically controllable, graphene layer. Demonstration of the integrated graphene plasmon laser principle lays the foundation for a new generation of active, programmable plasmonic metamaterials with major implications across photonics, material sciences, and nanotechnology.

  7. Stability Analysis of Networked Control Systems With Aperiodic Sampling and Time-Varying Delay.

    Science.gov (United States)

    Chen, Jie; Meng, Su; Sun, Jian

    2016-12-01

    This paper addresses the stability of networked control systems with aperiodic sampling and time-varying network-induced delay. The sampling intervals are assumed to vary within a known interval. The transmission delay is assumed to belong to a given interval. The closed-loop system is first converted to a discrete-time system with multiple time-varying delays and norm-bounded uncertainties resulting from the variation of the sampling intervals. And then, it is transformed into a delay-free system being form of an interconnection of two subsystems. By utilizing scaled small gain theorem, an asymptotic stability criterion for the closed-loop system is proposed in terms of linear matrix inequality. Finally, numerical examples demonstrate the effectiveness of the proposed method and its advantages over existing methods.

  8. Evidence of parameter-induced aperiodic stochastic resonance with fixed noise

    Institute of Scientific and Technical Information of China (English)

    Li Jian-Long

    2007-01-01

    Stochastic resonance (SR) is based on the cooperative effect between the stochastic dynamical system and the external forcing. As is well known, the cooperative effect is produced by adding noises. In this paper, we show the evidence that by changing the system parameters and the signal intensity, a nonlinear system in the presence of an input aperiodic signal can yield the cooperative effect, with the noise fixed. To quantify the nonlinear system output,we determine the theoretical bit error rate (BER). By numerical simulation, the validity of the theoretical derivation is checked. Besides, we show that parameter-induced SR is more realizable than SR via adding noises, especially when the noise intensity exceeds the resonance level, or when the characteristic of the noise is not known.

  9. Velocity Fluctuations Driven by the Damped, Aperiodic Mode in the Intergalactic Medium

    Science.gov (United States)

    Kolberg, U.; Schlickeiser, R.; Yoon, P. H.

    2017-08-01

    On account of its finite temperature, the unmagnetized intergalactic medium (IGM) is subject to thermal fluctuations. Due to the fundamental coupling between particles and fields in a plasma, the field fluctuations generate current densities by means of the Lorentz force and thereby affect both the density and the velocity fluctuations of the particles. Recently, a new damped, aperiodic mode was discovered that dominates field fluctuations in the IGM. Apart from its impact on the transport properties of the IGM that determine the propagation of cosmic rays, previous research has shown that this mode provides turbulent magnetic seed fields of 6× {10}-18 {{G}} that are an essential ingredient in the generation of cosmic magnetic fields. The current investigation addresses the influence of the mode on the particle motion. In order to describe the corresponding state of the turbulence, both the spectrum and the integrated total value of the mode-driven proton velocity fluctuations are computed. It is found that the latter amounts to 1.16× {10}8{ T}47/2{n}-7-1/2 {cm} {{{s}}}-1 assuming a temperature of {T}e={T}p={10}4{T}4 {{K}} and a density of {n}e={n}p={10}-7{n}-7 {{cm}}-3. This value is two orders of magnitude larger than the thermal velocity. If the IGM neutrals adopt the same velocities as the protons by mutual charge exchange and elastic collisions (ambipolar diffusion), atomic lines propagating through the IGM are expected to display spectral broadening, enhanced by a factor of 90 beyond the thermal level in the case of hydrogen. This opens the window to a first direct observation of the damped aperiodic mode. Other observational techniques such as dispersion measure, rotation measure, and scintillation data are not applicable in this case because the mode is a transverse one, and, as such, it does not induce the required density fluctuations, as is shown here.

  10. Critical comparison of three modal methods: bidirectional eigenmode expansion propagation method, aperiodic rigorous coupled mode analysis, and harmonic expansion method

    Science.gov (United States)

    Ctyroký, Jirí; Richter, Ivan; Kwiecien, Pavel

    2008-06-01

    The performance of three bidirectional modal methods the "classical" bidirectional eigenmode expansion propagation method, the aperiodic rigorous coupled wave analysis (known also as the Fourier modal method), and the mode expansion method based on harmonic expansion are mutually compared using modeling tasks that include eigenmode calculation of a relatively high-contrast planar waveguide, spectral transmittance of a one-dimensional "photonic crystal" filter in a photonic wire, spectral transmittance of a surface plasmon based optical sensor, and a reflectance from a double-groove structure in a high-contrast waveguide. All methods exhibit generally comparable performance, as follows from good mutual agreement of the results and generally comparable computational time. Although all methods use perfectly matched layers as absorbing boundary conditions, their implementation in the aperiodic rigorous coupled wave analysis exhibits significantly stronger attenuation than that used in the other two methods. Thus, significant improvement of the latter methods seems possible.

  11. Aperiodic TiO2 nanotube photonic crystal: full-visible-spectrum solar light harvesting in photovoltaic devices.

    Science.gov (United States)

    Guo, Min; Xie, Keyu; Wang, Yu; Zhou, Limin; Huang, Haitao

    2014-09-23

    Bandgap engineering of a photonic crystal is highly desirable for photon management in photonic sensors and devices. Aperiodic photonic crystals (APCs) can provide unprecedented opportunities for much more versatile photon management, due to increased degrees of freedom in the design and the unique properties brought about by the aperiodic structures as compared to their periodic counterparts. However, many efforts still remain on conceptual approaches, practical achievements in APCs are rarely reported due to the difficulties in fabrication. Here, we report a simple but highly controllable current-pulse anodization process to design and fabricate TiO2 nanotube APCs. By coupling an APC into the photoanode of a dye-sensitized solar cell, we demonstrate the concept of using APC to achieve nearly full-visible-spectrum light harvesting, as evidenced by both experimental and simulated results. It is anticipated that this work will lead to more fruitful practical applications of APCs in high-efficiency photovoltaics, sensors and optoelectronic devices.

  12. Efficient conversion from infrared to red light by cascaded nonlinear optical processes using an aperiodically poled lithium niobate crystal

    Directory of Open Access Journals (Sweden)

    Juan Eduardo González

    2015-12-01

    Full Text Available We present a scheme for conversion of pulsed light from the infrared to the red spectral region, using an aperiodically poled ferroelectric crystal within a resonant cavity in which two cascaded nonlinear optical processes occur when pumped with a pulsed Nd:YAG laser. This device emits 9 ns pulses of over 1 mJ at 710 nm and is a viable source for future biomedical applications.

  13. A new class of aperiodic, long-range ordered artificial spin ices based upon Fibonacci distortions of 2D periodic lattices

    Science.gov (United States)

    Woods, Justin; Bhat, Vinayak; Farmer, Barry; Sklenar, Joseph; Teipel, Eric; Ketterson, John; Hastings, J. Todd; de Long, Lance

    2015-03-01

    Artificial spin ice (ASI) systems are composed of nanoscale ferromagnetic segments whose shape anisotropy dictates they behave as mesoscopic Ising spins. Most ASI have segments patterned on periodic lattices and a single vertex topology. We have continuously distorted 2D honeycomb and square lattices such that the pattern vertex spacings follow a Fibonacci chain sequence along primitive lattice directions. The Fibonacci distortion is related to the aperiodic translational symmetry of 2D artificial quasicrystals1 that cannot be viewed as continuous distortions of periodic lattices due to their forbidden (e.g., fivefold) rotational symmetries. In contrast, Fibonacci distortions of 2D periodic lattices can be ``turned on'' by control of the ratio of two lattice parameters d1 and d2. Distortions alter film segments such that pattern vertices are no longer equivalent and traditional spin ice rules are no longer strictly valid. We have performed OOMMF simulations of magnetization reversal for samples having different levels of distortion, and found the magnetic reversal to be dramatically slowed by small distortions (d1/d2 ~ 1). Research at Kentucky is supported by U.S. DoE Grant DE-FG02-97ER45653 and NSF Grant EPS-0814194.

  14. Cosmic magnetization: from spontaneously emitted aperiodic turbulent to ordered equipartition fields.

    Science.gov (United States)

    Schlickeiser, R

    2012-12-28

    It is shown that an unmagnetized nonrelativistic thermal electron-proton plasma spontaneously emits aperiodic turbulent magnetic field fluctuations of strength |δB|=3.5β(e)g(1/3)W(e)(1/2)  G, where β(e) is the normalized thermal electron temperature, W(e) the thermal plasma energy density, and g the plasma parameter. For the unmagnetized intergalactic medium, immediately after the reionization onset, the field strengths from this mechanism are about 2×10(-16)  G in cosmic voids and 2×10(-10)  G in protogalaxies, both too weak to affect the dynamics of the plasma. Accounting for simultaneous viscous damping reduces these estimates to 2×10(-21)  G in cosmic voids and 2×10(-12)  G in protogalaxies. The shear and/or compression of the intergalactic and protogalactic medium exerted by the first supernova explosions locally amplify these seed fields and make them anisotropic, until the magnetic restoring forces affect the gas dynamics at ordered plasma betas near unity.

  15. Optimized aperiodic multilayer structures for use as narrow-angular absorbers

    Energy Technology Data Exchange (ETDEWEB)

    Granier, Christopher H., E-mail: cgrani1@lsu.edu; Dowling, Jonathan P. [Department of Physics and Astronomy, Hearne Institute of Theoretical Physics, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Afzal, Francis O. [Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Department of Physics, Truman State University, Kirksville, Missouri 63501,USA (United States); Lorenzo, Simón G. [Department of Physics and Astronomy, Hearne Institute of Theoretical Physics, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Reyes, Mario [Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Department of Physics, California State University, San Bernardino, California 92407 (United States); Department of Physics and Astronomy, Hearne Institute of Theoretical Physics, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Veronis, Georgios [Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); School of Electrical Engineering and Computer Science, Louisiana State University, Baton Rouge, Louisiana 70803 (United States)

    2014-12-28

    In this paper, we investigate aperiodic multilayer structures for use as narrow-angular absorbers. The layer thicknesses and materials are optimized using a genetic global optimization algorithm coupled to a transfer matrix code to maximize the angular selectivity in the absorptance at a single or multiple wavelengths. We first consider structures composed of alternating layers of tungsten and silicon or silica, and find that it is not possible to achieve angular selectivity in the absorptance with such structures. We next consider structures composed of alternating layers of silicon and silica, and show that when optimized they exhibit high angular selectivity in absorptance. In addition, as the angular selectivity in absorptance increases, the wavelength range of high angular selectivity also decreases. Optimizing the material composition of the multilayer structures, in addition to optimizing the layer thicknesses, leads to marginal improvement in angular selectivity. Finally, we show that by optimizing the absorptance of the multilayer structures at multiple wavelengths, we can obtain structures exhibiting almost perfect absorptance at normal incidence and narrow angular width in absorptance at these wavelengths. Similar to the structures optimized at a single wavelength, the wavelength range of high angularly selective absorptance is narrow.

  16. A novel scenario of aperiodical impacts appearance in the turbine draft tube

    Science.gov (United States)

    Alekseenko, S. V.; Kuibin, P. A.; Shtork, S. I.; Skripkin, S. G.; Sonin, V. I.; Tsoy, M. A.; Ustimenko, A. S.

    2016-11-01

    The swirling flow in the discharge cone of hydroturbine is characterized by various self-induced instabilities and associated low frequency phenomena when the turbine is operated far from the best efficiency point. In particular, the precessing vortex rope develops at part-load regimes in the draft tube. This rope can serve a reason of the periodical low- frequency pressure oscillations in the whole hydrodynamical system. During the experimental research of flow structure in the discharge cone in a regime of free runner new interesting phenomenon was discovered. Due to instability some coils of helical vortex close to each other and reconnection appears with generation of a vortex ring. The experiments were fulfilled at the cavitational conditions when a cavity arises in the vortex core. So the phenomenon was registered with help of visualization by the high speed video recording. The vortex ring after the reconnection moves apart from the main vortex rope toward the wall and downstream. When it reaches the area with high pressure the cavity collapses with generation of pressure impact. The mechanism of cavitational vortex rings generation and their further collapse can serve as a prototype of the aperiodical pressure impacts inside the turbine draft tube.

  17. Plastic Flowlike Deformation and Its Relation to Aperiodic Peaks in Conductance Histograms of Molybdenum Nanocontacts

    Science.gov (United States)

    Yamada, Kohei; Kizuka, Tokushi

    2016-10-01

    We observed the tensile deformation of molybdenum (Mo) nanocontacts (NCs) and simultaneously measured their conductance by in situ transmission electron microscopy. During deformation, the contact width decreased from several nanometers to a single-atom size. Mo NCs were thinned via a plastic flowlike deformation process. The process differs from the slip on lattice planes, which is frequently observed in NCs made of noble metals. We plotted histograms of the time-conductance traces measured during the tensile deformation of Mo NCs. In the conductance histograms, we observed peaks at 1.8G0 (G0 = 2e2/h, where e is the electron charge and h is Planck's constant), 3.6G0, and 4.4G0. When the minimum conductance (1.8G0) was measured, the minimum cross-sectional widths of the NCs were 3-7 atoms. These NCs exhibited relaxed structures that formed irregularly after the plastic flowlike deformation occurred in the final stage of the tensile process. We inferred that the aperiodic peaks observed in the conductance histograms originated from irregular variations in the contact areas and atomic configurations of the NCs during the plastic flowlike deformation. Moreover, the conductance value of the single-atom contacts was less than 0.1G0.

  18. Geometry optimizaion of aperiodic polymers by combining the elongation method with MOPAC program package

    Energy Technology Data Exchange (ETDEWEB)

    Mitani, Masaki; Aoki, Yuriko; Imamura, Akira [Hiroshima Univ. (Japan)

    1996-12-31

    Recently we have developed the elongation method, by which we can calculate the electronic structure of various types of periodic as well as aperiodic polymers with relatively much shorter computation time and much smaller memory size. The characteristic of the elongation method is to calculate the electronic structure of polymers by adding a monomer one by one as is the case for the polymerization reaction. The similar procedure can be applied to the geometry optimization of polymers in the frame of the elongation method, that is, the geometry optimization procedure is limited in a region in which the electronic structure changes against the elongation of the polymer. In this procedure, we can obtain the optimized geometry of the polymer efficiently with much smaller computation time. In the present study, we combined the elongation program with MOPAC program package which is used worldwide. The concrete geometry optimization procedure bases upon the Z-matrix procedure . When electron density on the relevant atoms does change its magnitude less than a threshold value, say 0.00001% against the elongation of the polymer, the corresponding geometrical parameters are thereafter fixed. For example, the length of the bond A-B is fixed when the electron densities on atoms A and B are frozen. The same procedure is applied to the bond angle and the dihedral angle. This optimization procedure were applied to polyethylene, polyacetylene, polyglycine and polyacetylene with positive and negative solitons. The calculated results are promising and this method is found to be reliable and applicable enough to be useful for the non-periodical polymers such as oligopeptides with various kinds of amino acid reridues. The obtained results will be given in the lecture in detail.

  19. Exponential synchronization of generalized neural networks with mixed time-varying delays and reaction-diffusion terms via aperiodically intermittent control

    Science.gov (United States)

    Gan, Qintao

    2017-01-01

    In this paper, the exponential synchronization problem of generalized reaction-diffusion neural networks with mixed time-varying delays is investigated concerning Dirichlet boundary conditions in terms of p-norm. Under the framework of the Lyapunov stability method, stochastic theory, and mathematical analysis, some novel synchronization criteria are derived, and an aperiodically intermittent control strategy is proposed simultaneously. Moreover, the effects of diffusion coefficients, diffusion space, and stochastic perturbations on the synchronization process are explicitly expressed under the obtained conditions. Finally, some numerical simulations are performed to illustrate the feasibility of the proposed control strategy and show different synchronization dynamics under a periodically/aperiodically intermittent control.

  20. The aperiodic X-ray variability of the accreting millisecond pulsar SAX J1808.4-3658

    CERN Document Server

    Bult, Peter

    2015-01-01

    We have studied the aperiodic variability of the 401 Hz accreting millisecond X-ray pulsar SAX J1808.4-3658 using the complete data set collected with the Rossi X-ray Timing Explorer over 14 years of observation. The source shows a number of exceptional aperiodic timing phenomena that are observed against a backdrop of timing properties that show consistent trends in all five observed outbursts and closely resemble those of other atoll sources. We performed a detailed study of the enigmatic ~410 Hz QPO, which has only been observed in SAX J1808.4-3658. We find that it appears only when the upper kHz QPO frequency is less than the 401 Hz spin frequency. The difference between the ~410 Hz QPO frequency and the spin frequency follows a similar frequency correlation as the low frequency power spectral components, suggesting that the ~410 Hz QPO is a retrograde beat against the spin frequency of a rotational phenomenon in the 9 Hz range. Comparing this 9 Hz beat feature with the Low-Frequency QPO in SAX J1808.4-36...

  1. Mo/Si aperiodic multilayer broadband reflective mirror for 12.5-28.5-nrn wavelength range

    Institute of Scientific and Technical Information of China (English)

    Moyan Tan; Haochuan Li; Qiushi Huang; Hongjun Zhou; Tonglin Huo; Xiaoqiang Wang; Jingtao Zhu

    2011-01-01

    @@ Aperiodic molybdenum/silicon (Mo/Si) multilayer designed as a broadband reflective mirror with mean reflectivity of 10% over a wide wavelength range of 12.5-28.5 nm at incidence angle of 5° is developed using a numerical optimized method. The multilayer is prepared using direct current magnetron sputtering technology. The reflectivity is measured using synchrotron radiation. The measured mean reflectivity is 7.0% in the design wavelength range of 12.5-28.5 nm. This multilayer broadband reflective mirror can be used in extreme ultraviolet measurements and will greatly simplify the experimental arrangements.%Aperiodic molybdenum/silicon (Mo/Si) multilayer designed as a broadband reflective mirror with mean reflectivity of 10% over a wide wavelength range of 12.5-28.5 nm at incidence angle of 5° is developed using a numerical optimized method. The multilayer is prepared using direct current magnetron sputtering technology. The reflectivity is measured using synchrotron radiation. The measured mean reflectivity is 7.0% in the design wavelength range of 12.5-28.5 nm. This multilayer broadband reflective mirror can be used in extreme ultraviolet measurements and will greatly simplify the experimental arrangements.

  2. A-periodic multilayer development for attosecond pulses in the 300-500 eV photon energy range

    Energy Technology Data Exchange (ETDEWEB)

    Guggenmos, Alexander; Hofstetter, Michael; Kleineberg, Ulf [Fakultaet fuer Physik, Ludwig-Maximilians-Universitaet Muenchen, Garching (Germany); Max-Planck-Institut fuer Quantenoptik, Garching (Germany); Rauhut, Roman [Fakultaet fuer Physik, Ludwig-Maximilians-Universitaet Muenchen, Garching (Germany)

    2011-07-01

    The development of ultrafast X-ray pulses in the sub-femtosecond time regime is a cutting edge technology for studying electron dynamics in atoms, molecules or solid surfaces/nanostructures by means of pump/probe electron spectroscopy. XUV elements as multilayer mirrors and thin metal filters are used to filter and shape attosecond bursts from high harmonic radiation. One near future goal is to extend the current technology to higher photon energies, reaching the water window range around 300-500 eV, where the in-vitro investigation of bio-materials on ultra-short time scales becomes possible. Following the ideas of nowadays experimental setups, both the spectral and the temporal resolution can be determined and guided by means of periodic and a-periodic multilayer mirrors, allowing for spectral and temporal soft X-ray pulse shaping. We will present first investigations of periodic and a-periodic multilayer XUV optics in that energy range of 300-400 eV and discuss their applications for filtering single attosecond pulses from High Harmonic radiation. Simulations and optimizations of various binary and ternary multilayer material systems as well as first experimental results achieved by Ion Beam Deposition and in-situ ellipsometry of the deposited nanolayers are demonstrated.

  3. New Lagrangian tools for describing transport in aperiodic time dependent flows: a case study of the Kuroshio current

    Science.gov (United States)

    Mancho, Ana M.; Mendoza, Carolina

    2009-11-01

    In recent years there has been a lot of progress in the application of dynamical systems concepts to the description of transport in oceanic flows. In these flows the classical dynamical system theory does not apply since they are aperiodic and finite-time defined. Recently, for describing these flows a new definition of distinguished trajectory has been proposed (Madrid & Mancho, Chaos, 2009). Distinguished trajectories act as organizing centres of the geometrical template of aperiodic time-dependent flows, like fixed points and periodic orbits do in time independent or periodic flows. The computation of distinguished trajectories makes use of a function M of which we show contains a lot of Lagrangian information. In this presentation I will discuss how the visualization of this function M, allows identifying relevant Lagrangian features at a glance. In particular we report an application to real altimetry data taken from satellite in the area of the Kuroshio current. The function M also determines the stable and unstable subspaces of the distinguished hyperbolic trajectories which are tangent to the invariant manifolds. From the computation of stable and unstable manifolds we report an accurate description of transport routes in this region.

  4. Generation and Correlation Characteristics of Complex Spreading Sequences for CDMA Wireless Communication

    Directory of Open Access Journals (Sweden)

    Poonam Goyal

    2013-07-01

    Full Text Available This paper presents complex spreading sequences (CSS for use in coded multiple access communication systems. The complex sequences such as Zadoff-Chu (ZC and Oppermann {&} Vucetic (OV are described here. These complex spreading sequences offers a very wide range of values for both auto-correlation (AC and cross-correlation (CC functions, allowing great flexibility in the selection of characteristics of sequence sets. The parameters such as mean-square aperiodic AC and CC values for various sequence sets are presented here

  5. Thirty-two phase sequences design with good autocorrelation properties

    Indian Academy of Sciences (India)

    S P Singh; K Subba Rao

    2010-02-01

    Polyphase Barker Sequences are finite length, uniform complex sequences; the magnitude of their aperiodic autocorrelation sidelobes are bounded by 1. Such sequences have been used in numerous real-world applications such as channel estimation, radar and spread spectrum communication. In this paper, thirty-two phase Barker sequences up to length 24 with an alphabet size of only 32 are presented. The sequences from length 25 to 289 have autocorrelation properties better than well-known Frank codes. Because of the complex structure the sequences are very difficult to detect and analyse by an enemy’s electronic support measures (ESMs). The synthesized sequences are promising for practical application to radar and spread spectrum communication systems. These sequences are found using the Modified Simulated Annealing Algorithm (MSAA). The convergence rate of the algorithm is good.

  6. MVB非周期信息的通信带宽分配策略研究%Study on bandwidth allocation strategy of MVB aperiodic communication

    Institute of Scientific and Technical Information of China (English)

    曾秋芬; 陈特放; 刘毅斌

    2011-01-01

    Both periodic and aperiodic messages are transmitted on multifunction vehicle bus (MVB). The transmission of periodic messages must comply with the strict real-time requirements and aperiodic messages are always made a random arrival. Bandwidth availability of MVB can be improved if the bandwidth is distributed reasonably. On analyzing the characteristics of every type of messages, two bandwidth allocation strategies of MVB aperiodic communication are proposed. In combination with the scheduling principles of aperiodic messages, the two bandwidth allocation strategies are researched and compared; the application scope of everystrategy is given.%多功能车辆总线MVB需要传送具有高实时性要求的周期信息和随机到达的非周期信息,合理分配相应信息带宽可以提高整个网络的通信带宽利用率.在分析各类信息特点的基础上,提出了非周期信息通信的两种带宽分配策略.结合MVB非周期信息的调度方法,对两种策略进行了分析研究和性能比较,给出了各种策略的适用范围.

  7. Parameter-adjusted stochastic resonance system for the aperiodic echo chirp signal in optimal FrFT domain

    Science.gov (United States)

    Lin, Li-feng; Yu, Lei; Wang, Huiqi; Zhong, Suchuan

    2017-02-01

    In order to improve the system performance for moving target detection and localization, this paper presents a new aperiodic chirp signal and additive noise driving stochastic dynamical system, in which the internal frequency has the linear variation matching with the driving frequency. By using the fractional Fourier transform (FrFT) operator with the optimal order, the proposed time-domain dynamical system is transformed into the equivalent FrFT-domain system driven by the periodic signal and noise. Therefore, system performance is conveniently analyzed from the view of output signal-to-noise ratio (SNR) in optimal FrFT domain. Simulation results demonstrate that the output SNR, as a function of system parameter, shows the different generalized SR behaviors in the case of various internal parameters of driving chirp signal and external parameters of the moving target.

  8. A molecular ;phase ordering; phase transition leading to a modulated aperiodic composite in n-heptane/urea

    Energy Technology Data Exchange (ETDEWEB)

    Mariette, C.; Huard, M.; Rabiller, P.; Nichols, Shane M.; Ecolivet, C.; Janssen, Ted; Alquist, III, Keith E.; Hollingsworth, Mark D.; Toudic, B. (CNRS-UMR); (Nijmegen); (KSU)

    2012-07-11

    n-Heptane/urea is an aperiodic inclusion compound in which the ratio of host and guest repeats along the channel axis is very close to unity and is found to have a constant value (0.981) from 280 K to 90 K. Below 280 K, two phase transitions are observed. The first (T{sub c1} = 145 K) is a ferroelastic phase transition that generates superstructure reflections for the host while leaving the guest with 1D order. The second (T{sub c2} = 130 K) is a 'phase ordering' transition to a four-dimensional structure (P2{sub 1}11(0{beta}{gamma})) with pronounced host-guest intermodulation and a temperature dependent phase shift between guests in adjacent channels.

  9. Leader-follower H∞ consensus of linear multi-agent systems with aperiodic sampling and switching connected topologies.

    Science.gov (United States)

    Zhang, Dan; Xu, Zhenhua; Wang, Qing-Guo; Zhao, Yun-Bo

    2017-02-12

    This paper is concerned with the distributed H∞ consensus of leader-follower multi-agent systems with aperiodic sampling interval and switching topologies. Under the assumption that the sampling period takes values from a given set, a new discrete-time model is proposed for the tracking error system. For the multi-agent systems with time-varying sampling period, switching topologies and external disturbance, the considered tracking problem is converted to a robust H∞ control problem. With help of the Lyapunov stability theory, a sufficient condition for the existence of mode-dependent controller is established and it guarantees the exponential stability of tracking error system and a prescribed H∞ disturbance attenuation level. The influence of sampling period on the overall control performance is also discussed. Two simulation examples are given to show the effectiveness of the proposed control algorithm.

  10. Determination of the Integrated Sidelobe Level of Sets of Rotated Legendre Sequences

    CERN Document Server

    Haboba, Salvador Javier; Setti, Gianluca

    2010-01-01

    Sequences sets with low aperiodic auto- and cross-correlations play an important role in many applications like communications, radar and other active sensing applications. The use of antipodal sequences reduces hardware requirements while increases the difficult of the task of signal design. In this paper we present a method for the computation of the Integrated Sidelobe Level (ISL), and we use it to calculate the asymptotic expression for the ISL of a set of sequences formed by different rotations of a Legendre sequence.

  11. TTCAN非周期信息概率延时分析及改进%Study and Improvement on Probability of TTCAN Aperiodic Message Delay

    Institute of Scientific and Technical Information of China (English)

    陶震宇; 夏继强; 满庆丰

    2014-01-01

    The period messages of time-triggered CAN ( TTCAN) bus system possess highly real-time performance,but the a-periodic message delay of low priority nodes doesn’ t decrease,and is even more serious compared with CAN under high loads. Probability theory was used to analyze the delay of TTCAN aperiodic message,and the calculation process was given.The method which inserted aperiodic information arbitration time slot between two adjacent exclusive windows was put forward to improve the real-time performance of the TTCAN aperiodic messages.Probabilistic delay of improved TTCAN aperiodic message was calculated, and period message delay was analyzed.The simulation calculation shows that the method proposed effectively reduces the aperiodic message delay and the period messages meet the real-time demand.%时间触发控制器局域网( TTCAN)总线保证了周期信息的实时性,但低优先级节点的非周期信息在高负载下延时未得到改善,甚至与CAN相比,其延时将增大。文中运用概率论分析了TTCAN非周期信息的延时及计算方法。提出在TTCAN的独占窗时间段插入非周期信息仲裁时隙,以提高非周期信息实时性。分析了改进后TTCAN非周期信息概率延时的计算方法,并给出了改进后周期信息延时分析。仿真计算说明文中提出的改进方法在满足周期信息实时性要求的情况下,有效提高了非周期信息的实时性。

  12. Analysis and prediction of aperiodic hydrodynamic oscillatory time series by feed-forward neural networks, fuzzy logic, and a local nonlinear predictor

    Energy Technology Data Exchange (ETDEWEB)

    Gentili, Pier Luigi, E-mail: pierluigi.gentili@unipg.it [Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia (Italy); Gotoda, Hiroshi [Department of Mechanical Engineering, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu-shi, Shiga 525-8577 (Japan); Dolnik, Milos; Epstein, Irving R. [Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110 (United States)

    2015-01-15

    Forecasting of aperiodic time series is a compelling challenge for science. In this work, we analyze aperiodic spectrophotometric data, proportional to the concentrations of two forms of a thermoreversible photochromic spiro-oxazine, that are generated when a cuvette containing a solution of the spiro-oxazine undergoes photoreaction and convection due to localized ultraviolet illumination. We construct the phase space for the system using Takens' theorem and we calculate the Lyapunov exponents and the correlation dimensions to ascertain the chaotic character of the time series. Finally, we predict the time series using three distinct methods: a feed-forward neural network, fuzzy logic, and a local nonlinear predictor. We compare the performances of these three methods.

  13. Composite Binary Sequences with a Large Ensemble and Zero Correlation Zone

    Directory of Open Access Journals (Sweden)

    S. S. Yudachev

    2015-01-01

    Full Text Available The article considers a proposed class of derived signals such as composite binary sequences for application in advanced spread spectrum radio systems of various purposes, using signals based on spectrum spreading by direct sequence method. Considered composite sequences, having a representative set of lengths and unique correlation properties, compares favorably with the widely used at present large ensembles formed on a single algorithmic basis. To evaluate the properties of the composite sequences generated on the basis of two components - the Barker code and Kerdock sequences, expressions of periodic and aperiodic correlation functions are given.An algorithm for generating practical ensembles of composite sequences is presented. On the basis of the algorithm and its software implementation in C #, the samples of the sequence ensembles of various lengths were obtained and their periodic and aperiodic correlation functions and statistical characteristics were studied in detail. As an illustration, some of the most typical correlation functions are presented. The most remarkable characteristics allowing a ssessing the feasibility of using this type of sequences in the design of specific types of radio systems are considered.On the basis of the proposed program and the performed calculations the conclusions can be drawn about the possibility of using the sequences of these classes, with the aim of reducing intra-system disturbance in the projected spread spectrum CDMA.

  14. On the area of accretion curtains from fast aperiodic time variability of the intermediate polar EX Hya

    CERN Document Server

    Semena, Andrey N; Buckley, David A H; Kotze, Marissa M; Khabibullin, Ildar I; Breytenbach, Hannes; Gulbis, Amanda A S; Coppejans, Rocco; Potter, Stephen B

    2014-01-01

    We present results of a study of the fast timing variability of the magnetic cataclysmic variable (mCV) EX Hya. It was previously shown that one may expect the rapid flux variability of mCVs to be smeared out at timescales shorter than the cooling time of hot plasma in the post shock region of the accretion curtain near the WD surface. Estimates of the cooling time and the mass accretion rate, thus provide us with a tool to measure the density of the post-shock plasma and the cross-sectional area of the accretion funnel at the WD surface. We have probed the high frequencies in the aperiodic noise of one of the brightest mCV EX Hya with the help of optical telescopes, namely SALT and the SAAO 1.9m telescope. We place upper limits on the plasma cooling timescale $\\tau<$0.3 sec, on the fractional area of the accretion curtain footprint $f<1.6\\times10^{-4}$, and a lower limit on the specific mass accretion rate $\\dot{M}/A \\gtrsim $3 g/sec/cm$^{-2}$. We show that measurements of accretion column footprints v...

  15. Radiation-disorder and aperiodicity in irradiated ceramics. Final technical report, 22 June 1989--21 June 1992

    Energy Technology Data Exchange (ETDEWEB)

    Hobbs, L.W.

    1992-07-01

    This final technical report documents the accomplishments of the program of research entitled ``Radiation Disorder and Aperiodicity in Irradiated Ceramics`` for the period June 22, 1989--June 21, 1992. This research forms the latest part on an on-going program, begun at MIT in 1983 under DOE support, which has had as its objectives investigation of the responses in radiation environments of ceramics heavily-irradiated with electrons, neutrons and ions, with potential applications to fusion energy technology and high-level nuclear waste storage. Materials investigated have included SiO{sub 2}, MgAl{sub 2}O{sub 4}, Al{sub 23}O{sub 27}N{sub 5}, SiC, BeO, LiAlO{sub 2}, Li{sub 2}ZrO{sub 3}, CaTiO{sub 3}KTaO{sub 3} and Ca(Zr, Pu)Ti{sub 2}O{sub 7}. The program initially proposed for 1989 had as its major objectives two main thrusts: (1) research on defect aggregation in irradiated non-oxide ceramics, and (2) research on irradiation-induced amorphization of network silicas and phosphates.

  16. ON THE BEAM INDUCED QUASI-INSTABILITY TRANSFORMATION OF THE DAMPED APERIODIC MODE IN THE INTERGALACTIC MEDIUM

    Energy Technology Data Exchange (ETDEWEB)

    Kolberg, U.; Schlickeiser, R. [Institut für Theoretische Physik, Lehrstuhl IV: Weltraum- and Astrophysik, Ruhr-Universität, Bochum (Germany); Yoon, P. H., E-mail: uk@tp4.rub.de, E-mail: rsch@tp4.rub.de, E-mail: yoonp@umd.edu [IPST, University of Maryland, College Park, Maryland 20742-2431 (United States)

    2016-02-01

    Highly relativistic electron–positron pair beams considerably affect the spontaneously emitted field fluctuations in the unmagnetized intergalactic medium (IGM). In view of the considered small density ratio of beam and background plasma, a perturbative treatment is employed in order to derive the spectral balance equations for the fluctuating fields from first principles of plasma kinetic theory that are covariantly correct within the limits of special relativity. They self-consistently account for the competing effects of spontaneous and induced emission and absorption in the perturbed thermal plasma. It is found that the presence of the beam transforms the growth rate of the dominating transverse damped aperiodic mode into an effective growth rate that displays positive values in certain spectral regions if beam velocity and wave vector are perpendicular or almost perpendicular to each other. This corresponds to a quasi-instability that induces an amplification of the fluctuations for these wavenumbers. Such an effect can greatly influence the cosmic magnetogenesis as it affects the strengths of the spontaneously emitted magnetic seed fields in the IGM, thereby possibly lowering the required growth time and effectivity of any further amplification mechanism such as an astrophysical dynamo.

  17. On the Beam Induced Quasi-instability Transformation of the Damped Aperiodic Mode in the Intergalactic Medium

    Science.gov (United States)

    Kolberg, U.; Schlickeiser, R.; Yoon, P. H.

    2016-02-01

    Highly relativistic electron-positron pair beams considerably affect the spontaneously emitted field fluctuations in the unmagnetized intergalactic medium (IGM). In view of the considered small density ratio of beam and background plasma, a perturbative treatment is employed in order to derive the spectral balance equations for the fluctuating fields from first principles of plasma kinetic theory that are covariantly correct within the limits of special relativity. They self-consistently account for the competing effects of spontaneous and induced emission and absorption in the perturbed thermal plasma. It is found that the presence of the beam transforms the growth rate of the dominating transverse damped aperiodic mode into an effective growth rate that displays positive values in certain spectral regions if beam velocity and wave vector are perpendicular or almost perpendicular to each other. This corresponds to a quasi-instability that induces an amplification of the fluctuations for these wavenumbers. Such an effect can greatly influence the cosmic magnetogenesis as it affects the strengths of the spontaneously emitted magnetic seed fields in the IGM, thereby possibly lowering the required growth time and effectivity of any further amplification mechanism such as an astrophysical dynamo.

  18. Evidence for deterministic chaos in aperiodic oscillations of acute lymphoblastic leukemia cells in long-term culture

    Science.gov (United States)

    Lambrou, George I.; Chatziioannou, Aristotelis; Vlahopoulos, Spiros; Moschovi, Maria; Chrousos, George P.

    Biological systems are dynamic and possess properties that depend on two key elements: initial conditions and the response of the system over time. Conceptualizing this on tumor models will influence conclusions drawn with regard to disease initiation and progression. Alterations in initial conditions dynamically reshape the properties of proliferating tumor cells. The present work aims to test the hypothesis of Wolfrom et al., that proliferation shows evidence for deterministic chaos in a manner such that subtle differences in the initial conditions give rise to non-linear response behavior of the system. Their hypothesis, tested on adherent Fao rat hepatoma cells, provides evidence that these cells manifest aperiodic oscillations in their proliferation rate. We have tested this hypothesis with some modifications to the proposed experimental setup. We have used the acute lymphoblastic leukemia cell line CCRF-CEM, as it provides an excellent substrate for modeling proliferation dynamics. Measurements were taken at time points varying from 24h to 48h, extending the assayed populations beyond that of previous published reports that dealt with the complex dynamic behavior of animal cell populations. We conducted flow cytometry studies to examine the apoptotic and necrotic rate of the system, as well as DNA content changes of the cells over time. The cells exhibited a proliferation rate of nonlinear nature, as this rate presented oscillatory behavior. The obtained data have been fit in known models of growth, such as logistic and Gompertzian growth.

  19. Application of non-uniform laxity to EDF for aperiodic tasks to improve task utilisation on multicore platforms

    CERN Document Server

    Kumar, K Pradheep

    2009-01-01

    This paper proposes a new scheduler applying the concept of non-uniform laxity to Earliest deadline first (EDF) approach for aperiodic tasks. This scheduler improves task utilisation (Execution time / deadline) and also increases the number of tasks that are being scheduled. Laxity is a measure of the spare time permitted for the task before it misses its deadline, and is computed using the expression (deadline - (current time + execution time)). Weight decides the priority of the task and is defined by the expression (quantum slice time / allocated time)*total core time for the task. Quantum slice time is the time actually used, allocated time is the time allocated by the scheduler, and total core time is the time actually reserved by the core for execution of one quantum of the task. Non-uniform laxity enables scheduling of tasks that have higher priority before the normal execution of other tasks and is computed by multiplying the weight of the task with its laxity. The algorithm presented in the paper has...

  20. The feasibility of MRI-guided whole prostate ablation with a linear aperiodic intracavitary ultrasound phased array

    Energy Technology Data Exchange (ETDEWEB)

    Sokka, S.D. [MIT Harvard Division of Health Sciences and Technology, Boston, MA 02115 (United States); Brigham and Women' s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115 (United States); Hynynen, K.H. [Brigham and Women' s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115 (United States)

    2000-11-01

    Over the past decade, numerous minimally invasive thermal procedures have been investigated to treat benign prostate hyperplasia and prostate cancer. Of these methods, ultrasound has shown considerable promise due to its ability to produce more precise and deeper thermal foci. In this study, a linear, transrectal ultrasound phased array capable of ablating large tissue volumes was fabricated and evaluated. The device was designed to be compatible for use with MRI guidance and thermometry. The intracavitary applicator increases treatable tissue volume by using an ultrasonic motor to provide a mechanical rotation angle of up to 100 deg. to a 62-element 1D ultrasound array. An aperiodic array geometry was used to reduce grating lobes. In addition, a specially designed Kapton interconnect was used to reduce cable crosstalk and hence also improve the acoustic efficiency of the array. MRI-guided in vivo and ex vivo experiments were performed to verify the array's large-volume ablative capabilities. Ex vivo bovine experiments were performed to assess the focusing range of the applicator. The array generated foci in a 3 cm (2 to 5 cm from the array surface along the axis normal to the array) by 5.5 cm (along the long axis of the array) by 6 cm (along the transverse axis of the array at a depth of 4 cm) volume. In vivo rabbit thigh experiments were performed to evaluate the lesion-producing capabilities in perfused tissue. The array generated 3 cm x 2 cm x 2 cm lesions with 8 to 12 half-minute sonications equally spaced in the volume. The results indicate that transrectal ultrasound coagulation of the whole prostate is feasible with the developed device. (author)

  1. Attributes of direct current aperiodic and alternating current harmonic components derived from large amplitude Fourier transformed voltammetry under microfluidic control in a channel electrode.

    Science.gov (United States)

    Matthews, Sinéad M; Shiddiky, Muhammad J A; Yunus, Kamran; Elton, Darrell M; Duffy, Noel W; Gu, Yunfeng; Fisher, Adrian C; Bond, Alan M

    2012-08-07

    The flow rate dependencies of the aperiodic direct current (dc) and fundamental to eighth alternating current (ac) harmonic components derived from large-amplitude Fourier transformed ac (FT-ac) voltammetry have been evaluated in a microfluidic flow cell containing a 25 μm gold microband electrode. For the oxidation of ferrocenemethanol ([FcMeOH]/[FcMeOH](+) process) in aqueous 0.1 M KNO(3) electrolyte, standard "Levich-like" dc behavior is observed for the aperiodic dc component, which enables the diffusion coefficient for FcMeOH to be obtained. In experimental studies, the first and second ac harmonic components contain contributions from the double layer capacitance current, thereby allowing details of the non-Faradaic current to be established. In contrast, the higher order harmonics and dc aperiodic component are essentially devoid of double layer capacitance contributions allowing the faradaic current dependence on flow rate to be studied. Significantly, flow rate independent data conforming to linear diffusion controlled theory are found in the sixth and higher ac harmonics at a frequency of 15 Hz and for all ac harmonics at a frequency of ≥ 90 Hz. Analysis of FT-ac voltammograms by theory based on stationary microband or planar electrode configurations confirms that stationary microband and planar electrode configurations and experimental data all converge for the higher order harmonics and establishes that the electrode kinetics are very fast (≥1 cms(-1)). The ability to locate, from a single experiment, a dc Faradaic component displaying Levich behavior, fundamental and second harmonics that contain details of the double layer capacitance, and Faradaic ac higher order harmonic currents that are devoid of capacitance, independent of the volume flow rate and also conform closely to mass transport by planar diffusion, provides enhanced flexibility in mass transport and electrode kinetic analysis and in understanding the performance of hydrodynamic

  2. Surprises in aperiodic diffraction

    CERN Document Server

    Baake, Michael

    2009-01-01

    Mathematical diffraction theory is concerned with the diffraction image of a given structure and the corresponding inverse problem of structure determination. In recent years, the understanding of systems with continuous and mixed spectra has improved considerably. Moreover, the phenomenon of homometry shows various unexpected new facets. Here, we report on some of the recent results in an exemplary and informal fashion.

  3. On the Properties of Reachability, Observability, Controllability, and Constructibility of Discrete-Time Positive Time-Invariant Linear Systems with Aperiodic Choice of the Sampling Instants

    Directory of Open Access Journals (Sweden)

    M. De la Sen

    2007-01-01

    Full Text Available This paper investigates the properties of reachability, observability, controllability, and constructibility of positive discrete-time linear time-invariant dynamic systems when the sampling instants are chosen aperiodically. Reachability and observability hold if and only if a relevant matrix defining each of those properties is monomial for the set of chosen sampling instants provided that the continuous-time system is positive. Controllability and constructibility hold globally only asymptotically under close conditions to the above ones guaranteeing reachability/observability provided that the matrix of dynamics of the continuous-time system, required to be a Metzler matrix for the system's positivity, is furthermore a stability matrix while they hold in finite time only for regions excluding the zero vector of the first orthant of the state space or output space, respectively. Some related properties can be deduced for continuous-time systems and for piecewise constant discrete-time ones from the above general framework.

  4. MVB非周期信息的实时能力分析%Realtime Capability Analysis of Aperiodic Message in MVB

    Institute of Scientific and Technical Information of China (English)

    曾秋芬; 陈特放; 刘毅斌

    2012-01-01

    The realtime performance of train network control system based on TCN is guaranteed by realtime capability of MVB. Worst-case response time is obtained by analyzing MVB traffic mechanism of aperiodic messages and the bandwidth shared by both periodic and aperiodic messages. The Calculation formulas of worst-case response time are established to every priority according to the various event-rounding mechanism. Meanwhile, An optimized strategy is proposed which, through verification, turns out to be an efficient way to improve the realtime capability of MVB.%MvB的实时能力是基于TCN的列车网络控制系统实时性能的重要保证,详细分析了MVB非周期信息的通信原理和调度流程,对仲裁延迟进行了具体的定义,在研究MVB周期信息和非周期信息带宽占用的基础上,给出了MVB非周期信息的最差情况响应时间.根据非周期信息的各种轮询机制,建立不同优先级的最差情况响应时间计算公式.在此基础上,提出了非周期信息实时能力优化策略,分析表明,该策略有效提高了MVB非周期信息的实时通信能力.

  5. EXPERIMENTAL RESEARCHES OF ELECTRO-THERMAL RESISTIBILITY OF SEND-OFFS AND CABLES TO ACTION RATIONED ON THE INTERNATIONAL STANDARD OF IEC 62305-1-2010 OF APERIODIC IMPULSE OF CURRENT OF ARTIFICIAL LIGHTNING

    OpenAIRE

    M.I. Baranov; Rudakov, S. V.

    2016-01-01

    Purpose. Experimental researches of electro-thermal resistibility of cable-explorer products, applied in the power electric circuits of objects of electric-power industry, to action on its copper and aluminum parts bearings a current rationed on the International Standard of IEC 62305-1-2010 aperiodic impulse 10/350 μs of current of artificial lightning. Methodology. Electrophysics bases of technique of high tensions and high pulsed currents (HPC), and also scientific and technical bases of p...

  6. Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences.

    Science.gov (United States)

    Derr, Julien; Manapat, Michael L; Rajamani, Sudha; Leu, Kevin; Xulvi-Brunet, Ramon; Joseph, Isaac; Nowak, Martin A; Chen, Irene A

    2012-05-01

    During the origin of life, the biological information of nucleic acid polymers must have increased to encode functional molecules (the RNA world). Ribozymes tend to be compositionally unbiased, as is the vast majority of possible sequence space. However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences. While natural selection could lead to complex sequences, molecules with some activity are required to begin this process. Was the emergence of compositionally diverse sequences a matter of chance, or could prebiotically plausible reactions counter chemical biases to increase the probability of finding a ribozyme? Our in silico simulations using a two-letter alphabet show that template-directed ligation and high concatenation rates counter compositional bias and shift the pool toward longer sequences, permitting greater exploration of sequence space and stable folding. We verified experimentally that unbiased DNA sequences are more efficient templates for ligation, thus increasing the compositional diversity of the pool. Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules. Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life.

  7. What did Erwin mean? The physics of information from the materials genomics of aperiodic crystals and water to molecular information catalysts and life.

    Science.gov (United States)

    Varn, D P; Crutchfield, J P

    2016-03-13

    Erwin Schrödinger famously and presciently ascribed the vehicle transmitting the hereditary information underlying life to an 'aperiodic crystal'. We compare and contrast this, only later discovered to be stored in the linear biomolecule DNA, with the information-bearing, layered quasi-one-dimensional materials investigated by the emerging field of chaotic crystallography. Despite differences in functionality, the same information measures capture structure and novelty in both, suggesting an intimate coherence between the information character of biotic and abiotic matter-a broadly applicable physics of information. We review layered solids and consider three examples of how information- and computation-theoretic techniques are being applied to understand their structure. In particular, (i) we review recent efforts to apply new kinds of information measures to quantify disordered crystals; (ii) we discuss the structure of ice I in information-theoretic terms; and (iii) we recount recent investigations into the structure of tris(bicyclo[2.1.1]hexeno)benzene, showing how an information-theoretic analysis yields additional insight into its structure. We then illustrate a new Second Law of Thermodynamics that describes information processing in active low-dimensional materials, reviewing Maxwell's Demon and a new class of molecular devices that act as information catalysts. Lastly, we conclude by speculating on how these ideas from informational materials science may impact biology.

  8. Effect of roughness, deterministic and random errors in film thickness on the reflecting properties of aperiodic mirrors for the EUV range

    Science.gov (United States)

    Gaikovich, P. K.; Polkovnikov, V. N.; Salashchenko, N. N.; Chkhalo, N. I.; Schäfers, F.; Sokolov, A.

    2016-05-01

    By the example of three aperiodic multilayer Mo/Si mirrors (AMM) for the wavelength ranges 17-21 nm, 24-29 nm, and 28-33 nm we have studied numerically the effect of the linearly determinisctic and random fluctuations of the film thickness and the interlayer roughness on the spectral dependences of the reflection coefficient. The simulation results are used to solve the inverse problem of reconstructing the interlayer roughness and the thickness of individual films from the measured dependences of the extreme UV radiation reflection coefficients. It is shown that the 'asymmetry' of the boundaries affects the magnitude and slope of the reflection coefficient plateau. Random fluctuations of the film thickness with the variance of 1%-2% weakly influence the reflection characteristics of AMMs and allow reliable reconstruction of the thickness of individual films. The fluctuations with the variance 8%-10% allow the estimation of individual thicknesses, but the reflection curve in this case strongly differs from the desirable one. Larger fluctuations do not allow the reconstruction of the AMM structure. The basic criteria for high-quality AMM synthesis are formulated.

  9. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  10. Concurrent cognitive processing and letter sequence transcription deficits in stutterers.

    Science.gov (United States)

    Webster, W G

    1990-03-01

    Previous research has indicated that men who stutter transcribe rapidly presented sequences of letters more slowly and less accurately than nonstutterer controls. Experiment 1 demonstrated that the transcription deficit is not limited to task conditions that demand concurrent monitoring and responding. This was evidenced by comparable deficits on a successive response condition that required subjects to write letters after the presentation was complete. The results of Experiment 2 indicated that the deficit is not due to a difficulty by stutterers in parsing streams of stimulus information internally. Their performance did not differentially improve when letters were grouped with brief pauses, nor with experience in transcribing preparsed letter sequences. This experiment also demonstrated that the phenomenon is generalizable to women. In related testing, stutterers were slower than controls in writing internally generated sequences of letters, those of the alphabet forwards and backwards, but not in writing the same two letters, A and B, repetitively nor in the cognitively more demanding task of writing numbers backwards by three's. These results parallel those obtained with finger tapping of same versus unique sequences by stutterers and were interpreted as being consistent with the idea that while stutterers are not generally slower motorically than nonstutterers, they experience difficulty when required to organize and carry out tasks with new multiple response transitions. The two experiments have replicated and extended, under different conditions, the earlier findings of a letter sequence transcription deficit in stutterers, but the nature of the interference still remains to be clarified.

  11. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies...

  12. The effect of non-linear capacitances in the localization properties of aperiodic dual electric transmission lines

    Science.gov (United States)

    Lazo, Edmundo; Garrido, Alejandro; Neira, Félix

    2016-11-01

    This study investigates the localization properties of dual electric transmission lines with non-linear capacitances. The VC,n voltage across each capacitor is selected as a non-linear function of the electric charge qn, i.e., VC,n = qn(1/Cn -ɛn|qn|2) where Cn is the linear part of the capacitance and ɛn the amplitude of the non-linear term. We follow a binary distribution of values of ɛn, according to the Thue-Morse m-tupling sequence. The localization behavior of this non-linear case indicates that the case m = 2 does not belong to the m ≥ 3, family because when m changes from m = 2 to m = 3, the number of extended states diminishes dramatically. This proves the topological difference of the m = 2 and m = 3 families. However, by increasing m values, localization behavior of the m-tupling family resembles that of the m = 2, case because the system begins to regain its extended states. The exact same result was obtained recently in the study of linear direct transmission lines with m-tupling distribution of inductances. Consequently, we state that the localization behavior of the m-tupling family as a function of the m value is independent of both the linear and the non-linear system under study, but independent of the kind of transmission line (dual or direct). This is curious behavior of the m-tupling family and thus deserves more scholarly attention.

  13. A powerful high-voltage generator of aperiodic impulses of current of artificial lightning with the peak-temporal parameters rated on an International Standard IEC 62305-1-2010

    Directory of Open Access Journals (Sweden)

    M.I. Baranov

    2015-03-01

    Full Text Available Created in accordance with the requirements of international standard of IEC 62305-1-2010 powerful high-voltage generator, forming on the low-resistance actively-inductive loading the aperiodic impulses of current of artificial lightning of the rationed temporal form 10 μs/350 μs and amplitudes of ±(100−200 кА with a foregoing standard by admittances set is presented and described. The results of practical approbation in the laboratory terms of this generator at the in-use electric loading with active resistance of 0.1 Ohm and inductance of 1,5 μH are presented.

  14. A POWERFUL HIGH-VOLTAGE GENERATOR OF APERIODIC IMPULSES OF CURRENT OF ARTIFICIAL LIGHTNING WITH THE PEAK-TEMPORAL PARAMETERS RATED ON AN INTERNATIONAL STANDARD IEC 62305-1-2010

    OpenAIRE

    M.I. Baranov; G.M. Koliushko; V.I. Kravchenko; Rudakov, S. V.

    2015-01-01

    Created in accordance with the requirements of international standard of IEC 62305-1-2010 powerful high-voltage generator, forming on the low-resistance actively-inductive loading the aperiodic impulses of current of artificial lightning of the rationed temporal form 10 μs/350 μs and amplitudes of ±(100−200) кА with a foregoing standard by admittances set is presented and described. The results of practical approbation in the laboratory terms of this generator at the in-use electric loading w...

  15. A powerful high-voltage generator of aperiodic impulses of current of artificial lightning with the peak-temporal parameters rated on an International Standard IEC 62305-1-2010

    OpenAIRE

    M.I. Baranov; G.M. Koliushko; V.I. Kravchenko; Rudakov, S. V.

    2015-01-01

    Created in accordance with the requirements of international standard of IEC 62305-1-2010 powerful high-voltage generator, forming on the low-resistance actively-inductive loading the aperiodic impulses of current of artificial lightning of the rationed temporal form 10 μs/350 μs and amplitudes of ±(100−200) кА with a foregoing standard by admittances set is presented and described. The results of practical approbation in the laboratory terms of this generator at the in-use electric loading w...

  16. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  17. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  18. Three subsets of sequence complexity and their relevance to biopolymeric information

    Directory of Open Access Journals (Sweden)

    Trevors Jack T

    2005-08-01

    Full Text Available Abstract Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC, ordered (OSC, and functional (FSC. FSC alone provides algorithmic instruction. Random and Ordered Sequence Complexities lie at opposite ends of the same bi-directional sequence complexity vector. Randomness in sequence space is defined by a lack of Kolmogorov algorithmic compressibility. A sequence is compressible because it contains redundant order and patterns. Law-like cause-and-effect determinism produces highly compressible order. Such forced ordering precludes both information retention and freedom of selection so critical to algorithmic programming and control. Functional Sequence Complexity requires this added programming dimension of uncoerced selection at successive decision nodes in the string. Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC or low-informational self-ordering phenomena (OSC.

  19. Optimization of binary sequences based on evolutionary algorithm%基于进化计算的二元序列优化算法研究

    Institute of Scientific and Technical Information of China (English)

    李鹤; 李琦; 高军萍; 雷明然

    2014-01-01

    具有良好非周期自相关特性二元序列在通信同步、雷达等领域具有广泛的应用。通过对遗传算法、粒子群算法与量子粒子群算法三种进化算法进行对比分析,设计了具有良好非周期自相关特性的二元序列的搜索算法。研究结果表明,粒子群算法的搜索能力优于遗传算法,而量子粒子群算法具有参数少,易于控制的优点,取得了较好的优化结果。%Binary sequences with good aperiodic autocorrelation features are widely used in the field of radar, communication synchronization. Genetic algorithm, particle swarm optimization and quantum particle swarm optimization algorithm are compared and analyzed in this paper. The new search algorithm of binary sequences with good aperiodic autocorrelation properties are designed based on three evolutionary algorithms. Research results show that the search ability of particle swarm algorithm is better than genetic algorithm. Quantum particle swarm optimization algorithm has less parameters, easy to control, and the better good optimization results were obtained.

  20. The algorithm of random length sequences synthesis for frame synchronization of digital television systems

    Directory of Open Access Journals (Sweden)

    Аndriy V. Sadchenko

    2015-12-01

    Full Text Available Digital television systems need to ensure that all digital signals processing operations are performed simultaneously and consistently. Frame synchronization dictated by the need to match phases of transmitter and receiver so that it would be possible to identify the start of a frame. As a frame synchronization signals are often used long length binary sequence with good aperiodic autocorrelation function. Aim: This work is dedicated to the development of the algorithm of random length sequences synthesis. Materials and Methods: The paper provides a comparative analysis of the known sequences, which can be used at present as synchronization ones, revealed their advantages and disadvantages. This work proposes the algorithm for the synthesis of binary synchronization sequences of random length with good autocorrelation properties based on noise generator with a uniform distribution law of probabilities. A "white noise" semiconductor generator is proposed to use as the initial material for the synthesis of binary sequences with desired properties. Results: The statistical analysis of the initial implementations of the "white noise" and synthesized sequences for frame synchronization of digital television is conducted. The comparative analysis of the synthesized sequences with known ones was carried out. The results show the benefits of obtained sequences in compare with known ones. The performed simulations confirm the obtained results. Conclusions: Thus, the search algorithm of binary synchronization sequences with desired autocorrelation properties received. According to this algorithm, the sequence can be longer in length and without length limitations. The received sync sequence can be used for frame synchronization in modern digital communication systems that will increase their efficiency and noise immunity.

  1. EXPERIMENTAL RESEARCHES OF ELECTRO-THERMAL RESISTIBILITY OF SEND-OFFS AND CABLES TO ACTION RATIONED ON THE INTERNATIONAL STANDARD OF IEC 62305-1-2010 OF APERIODIC IMPULSE OF CURRENT OF ARTIFICIAL LIGHTNING

    Directory of Open Access Journals (Sweden)

    M.I. Baranov

    2016-03-01

    Full Text Available Purpose. Experimental researches of electro-thermal resistibility of cable-explorer products, applied in the power electric circuits of objects of electric-power industry, to action on its copper and aluminum parts bearings a current rationed on the International Standard of IEC 62305-1-2010 aperiodic impulse 10/350 μs of current of artificial lightning. Methodology. Electrophysics bases of technique of high tensions and high pulsed currents (HPC, and also scientific and technical bases of planning of devices of high-voltage impulsive technique and measuring HPC in them. Results. Experimental a way the quantitative levels of maximal values maximum of possible and critical closenesses of aperiodic impulse 10/350 μs of current of artificial lightning with rationed on the international standard of IEC 62305-1-2010 peak-temporal parameters and admittances on them in copper (aluminum parts bearings a current of send-offs and cables with a polyethylene (PET and polyvinylchloride (PVCH isolation. Originality. First in world practice on the unique powerful high-voltage generator of HPC of artificial lightning experimental researches of resistibility to lightning of pre-production models of send-offs (cables are conducted with copper (aluminum tendons, PET and PVCH by an isolation, in-use in power electric circuits of electric-power industry objects. Practical value. The use in practice of protecting from lightning of the got results will allow substantially to promote functional and fire-prevention safety of engineering communications of objects of industrial electroenergy in the conditions of action on them of short shots of linear lightning.

  2. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Nucleotide Sequence Nucleotide sequence of full length cDNA (trimmed sequence) kome_ine_full_seq...uence_db.fasta.zip kome_ine_full_sequence_db.zip kome_ine_full_sequence_db ...

  3. Classifying Genomic Sequences by Sequence Feature Analysis

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hua Liu; Dian Jiao; Xiao Sun

    2005-01-01

    Traditional sequence analysis depends on sequence alignment. In this study, we analyzed various functional regions of the human genome based on sequence features, including word frequency, dinucleotide relative abundance, and base-base correlation. We analyzed the human chromosome 22 and classified the upstream,exon, intron, downstream, and intergenic regions by principal component analysis and discriminant analysis of these features. The results show that we could classify the functional regions of genome based on sequence feature and discriminant analysis.

  4. Self-Triggered Model Predictive Control for Linear Systems Based on Transmission of Control Input Sequences

    Directory of Open Access Journals (Sweden)

    Koichi Kobayashi

    2016-01-01

    Full Text Available A networked control system (NCS is a control system where components such as plants and controllers are connected through communication networks. Self-triggered control is well known as one of the control methods in NCSs and is a control method that for sampled-data control systems both the control input and the aperiodic sampling interval (i.e., the transmission interval are computed simultaneously. In this paper, a self-triggered model predictive control (MPC method for discrete-time linear systems with disturbances is proposed. In the conventional MPC method, the first one of the control input sequence obtained by solving the finite-time optimal control problem is sent and applied to the plant. In the proposed method, the first some elements of the control input sequence obtained are sent to the plant, and each element is sequentially applied to the plant. The number of elements is decided according to the effect of disturbances. In other words, transmission intervals can be controlled. Finally, the effectiveness of the proposed method is shown by numerical simulations.

  5. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Amino Acid Sequence Amino Acid sequence of full length cDNA (Longest ORF) kome_ine_full_seq...uence_amino_db.fasta.zip kome_ine_full_sequence_amino_db.zip kome_ine_full_sequence_amino_db ...

  6. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  7. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  8. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence.

  9. Aperiodicity resulting from two-cycle coupling in the Belousov-Zhabotinskii reaction. III. Analysis of a model of the effect of spatial inhomogeneities at the input ports of a continuous-flow, stirred tank reactor

    Science.gov (United States)

    Györgyi, László; Field, Richard J.

    1989-11-01

    Deterministic chaos is a well-established phenomenon in continuous-flow, stirred tank reactor (CSTR) experiments with the oscillatory Belousov-Zhabotinskii (BZ) reaction. However, it has not yet been possible to reproduce the experimentally observed, robust chaos in simulations using realistic models of the homogeneous chemical kinetics of the BZ reaction. That it may be necessary to consider spatial inhomogeneities in modeling the BZ chaos is suggested by the existence of strong stirring effects on the aperiodic behavior and by the difficulty of reproducing chaos under the same conditions in reactors of different physical configuration. Such inhomogeneity might result from a lack of perfect mixing in the CSTR, especially near the inlets, or from diffusion of species at low flow rates from the CSTR reaction mixture into the tips of the inlets. The presence of spatial inhomogeneities allows coupling between essentially independent oscillators, a well-known source of chaos. Such a model using a realistic representation of the BZ kinetics leads to an eight-variable set of ordinary differential equations. Numerical analysis of these equations by continuation methods and by numerical integration shows the existence of broad regions of chaos and various hysteresis effects involving limit cycles, a steady state and/or a strange attractor. Tristability was found in calculations in a narrow flow rate range. The computed behavior appears for parameter values closely related to the values used experimentally to obtain similar phenomena, and the visual similarity of the computed and experimental strange attractors is striking. The experimental routes to chaos, period doubling, intermittency, and secondary Hopf bifurcations are all reproduced in the simulations. The computed and experimental structures of periodic windows observed within chaotic regions also are very similar.

  10. Kaks kirja vennale = Two Letters from Vincent van Gogh to his brother / Vincent van Gogh

    Index Scriptorium Estoniae

    Gogh, Vincent van, 1853-1890

    2008-01-01

    Kunstnik Vincent van Goghi kaks kirja oma vennale Theole. Tõlge vene keelest ja kommentaar Mehis Heinsaarelt. Ingliskeelsed kirjad raamatust "The Complete Letters of Vincent van Gogh", Thames and Hudson, 1979

  11. Kaks kirja vennale = Two Letters from Vincent van Gogh to his brother / Vincent van Gogh

    Index Scriptorium Estoniae

    Gogh, Vincent van, 1853-1890

    2008-01-01

    Kunstnik Vincent van Goghi kaks kirja oma vennale Theole. Tõlge vene keelest ja kommentaar Mehis Heinsaarelt. Ingliskeelsed kirjad raamatust "The Complete Letters of Vincent van Gogh", Thames and Hudson, 1979

  12. Coordinate cytokine regulatory sequences

    Science.gov (United States)

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

    2005-05-10

    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  13. A Wide-Field Survey for Transiting Hot Jupiters and Eclipsing Pre-Main-Sequence Binaries in Young Stellar Associations

    CERN Document Server

    Oelkers, Ryan J; Marshall, Jennifer L; DePoy, Darren L; Lambas, Diego G; Colazo, Carlos; Stringer, Katelyn

    2016-01-01

    The past two decades have seen a significant advancement in the detection, classification and understanding of exoplanets and binaries. This is due, in large part, to the increase in use of small-aperture telescopes (< 20 cm) to survey large areas of the sky to milli-mag precision with rapid cadence. The vast majority of the planetary and binary systems studied to date consist of main-sequence or evolved objects, leading to a dearth of knowledge of properties at early times (< 50 Myr). Only a dozen binaries and one candidate transiting Hot Jupiter are known among pre-main sequence objects, yet these are the systems that can provide the best constraints on stellar formation and planetary migration models. The deficiency in the number of well-characterized systems is driven by the inherent and aperiodic variability found in pre-main-sequence objects, which can mask and mimic eclipse signals. Hence, a dramatic increase in the number of young systems with high-quality observations is highly desirable to gui...

  14. Two-dimensional deterministic photonic band gap structures based on the quasiperiodic sequences at millimeter wave frequencies

    Directory of Open Access Journals (Sweden)

    Y. Trabelsi

    2011-08-01

    Full Text Available Two-dimensional quasi-periodic band gap structures were investigated theoretically in microwave frequency range. Quasiperiodic photonic crystal based on the square range, arranged in a quasi-periodical fashion which follows Thue Morse or Fibonaci period substitutional sequences were obtained by the inflation rules emerging from the quasi-periodic sequence. The introduction of 2D quasi-periodicity distribution like Thue Morse or Fibonacci order and deterministic aperiodicity give some interesting microwave properties and offers amultitude of adjacent pseudo-band gap in different frequency range. The potential of photonic structures are explored by varying the structural parameters. The photonic band gap formation was explored as function of geometries of the structures such as pillar radius and parameters of quasi-periodical sequences. The electromagnetic field distribution can be described as a quasi-localized state varied by some defect carried by Thue Morse order. These structures provide interesting properties, which could be used to design novelmicrowave devices.

  15. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  16. Contamination of sequence databases with adaptor sequences

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D. [National Institute of Mental Health, Bethesda, MD (United States)

    1997-02-01

    Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable of transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.

  17. Automated DNA Sequencing System

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  18. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  19. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  20. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  1. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  2. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  3. Enhanced virome sequencing using targeted sequence capture.

    Science.gov (United States)

    Wylie, Todd N; Wylie, Kristine M; Herter, Brandi N; Storch, Gregory A

    2015-12-01

    Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.

  4. DNA sequences encoding erythropoietin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, F.K.

    1987-10-27

    A purified and isolated DNA sequence is described consisting essentially of a DNA sequence encoding a polypeptide having an amino acid sequence sufficiently duplicative of that of erythropoietin to allow possession of the biological property of causing bone marrow cells to increase production of reticulocytes and red blood cells, and to increase hemoglobin synthesis or iron uptake.

  5. Low autocorrelation binary sequences

    Science.gov (United States)

    Packebusch, Tom; Mertens, Stephan

    2016-04-01

    Binary sequences with minimal autocorrelations have applications in communication engineering, mathematics and computer science. In statistical physics they appear as groundstates of the Bernasconi model. Finding these sequences is a notoriously hard problem, that so far can be solved only by exhaustive search. We review recent algorithms and present a new algorithm that finds optimal sequences of length N in time O(N {1.73}N). We computed all optimal sequences for N≤slant 66 and all optimal skewsymmetric sequences for N≤slant 119.

  6. Repdigits in -Lucas Sequences

    Indian Academy of Sciences (India)

    Jhon J J Bravo; Florian Luca

    2014-05-01

    For an integer ≥ 2, let $(L_n^{(k)})_n$ be the -Lucas sequence which starts with $0,\\ldots,0,2,1$ ( terms) and each term afterwards is the sum of the preceding terms. In 2000, Luca (Port. Math. 57(2) 2000 243-254) proved that 11 is the largest number with only one distinct digit (the so-called repdigit) in the sequence $(L_n^{(2)})_n$. In this paper, we address a similar problem in the family of -Lucas sequences. We also show that the -Lucas sequences have similar properties to those of -Fibonacci sequences and occur in formulae simultaneously with the latter.

  7. On Maximal Green Sequences

    CERN Document Server

    Brüstle, Thomas; Pérotin, Matthieu

    2012-01-01

    Maximal green sequences are particular sequences of quiver mutations which were introduced by Keller in the context of quantum dilogarithm identities and independently by Cecotti-Cordova-Vafa in the context of supersymmetric gauge theory. Our aim is to initiate a systematic study of these sequences from a combinatorial point of view. Interpreting maximal green sequences as paths in various natural posets arising in representation theory, we prove the finiteness of the number of maximal green sequences for cluster finite quivers, affine quivers and acyclic quivers with at most three vertices. We also give results concerning the possible numbers and lengths of these maximal green sequences. Finally we describe an algorithm for computing maximal green sequences for arbitrary valued quivers which we used to obtain numerous explicit examples that we present.

  8. Periodic and aperiodic plasmon lattice lasers

    NARCIS (Netherlands)

    Schokker, A.H.

    2016-01-01

    Motivated by seminal proposals for surface plasmon amplification by stimulated emission, we conduct experiments on 2D plasmonic particle arrays in waveguiding layers that provide gain. We find that purely periodic plasmonic particle systems provide lasing characteristics similar to DFB lasers, yet

  9. Aperiodicity Correction for Rotor Tip Vortex Measurements

    Science.gov (United States)

    2011-05-01

    Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 Wire Anemometry (HWA), see, e.g., Refs. 1–5. Further- more, for such point measurement techniques...components along x- and y-axis, ms−1 uc, vc Vortex convection velocities, ms−1 Vθ Swirl velocity, ms−1 x, y, z Measurement coordinate system, mm xc, yc...techniques such LDV and Hot - 1 Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of information is

  10. Deterministic Aperiodic Sickle Cell Blood Flows

    Science.gov (United States)

    Atsaves, Louis; Harris, Wesley

    2013-11-01

    In this paper sickle cell blood flow in the capillaries is modeled as a hydrodynamical system. The hydrodynamical system consists of the axisymmetric unsteady, incompressible Navier-Stokes equations and a set of constitutive equations for oxygen transport. Blood cell deformation is not considered in this paper. The hydrodynamical system is reduced to a system of non-linear partial differential equations that are then transformed into a system of three autonomous non-linear ordinary differential equations and a set of algebraic equations. We examine the hydrodynamical system to discern stable/unstable, periodic/nonperiodic, reversible/irreversible properties of the system. The properties of the solutions are driven in large part by the coefficients of the governing system of equations. These coefficients depend on the physiological properties of the sickle cell blood. The chaotic nature of the onset of crisis in sickle cell patients is identified. Research Assistant.

  11. A model for aperiodicity in earthquakes

    Directory of Open Access Journals (Sweden)

    B. Erickson

    2008-01-01

    Full Text Available Conditions under which a single oscillator model coupled with Dieterich-Ruina's rate and state dependent friction exhibits chaotic dynamics is studied. Properties of spring-block models are discussed. The parameter values of the system are explored and the corresponding numerical solutions presented. Bifurcation analysis is performed to determine the bifurcations and stability of stationary solutions and we find that the system undergoes a Hopf bifurcation to a periodic orbit. This periodic orbit then undergoes a period doubling cascade into a strange attractor, recognized as broadband noise in the power spectrum. The implications for earthquakes are discussed.

  12. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    the feasibility of predicting the fetal KEL1 phenotype using next-generation sequencing (NGS) technology. STUDY DESIGN AND METHODS: The KEL1/2 single-nucleotide polymorphism was polymerase chain reaction (PCR) amplified with one adjoining base, and the PCR product was sequenced using a genome analyzer (GAIIx......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...

  13. Hardware bitstream sequence recognizer

    OpenAIRE

    Karpin, Oleksandr; Sokil, Volodymyr

    2009-01-01

    This paper describes how to implement in hardware a bistream sequence recognizer using the PSoC Pseudo Random Sequence Generator (PRS) User Module. The PRS can be used in digital communication systems with the serial data interface for automatic preamble detection and extraction, control words selection, etc.

  14. Cosmetology: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  15. DNA sequencing by CE.

    Science.gov (United States)

    Karger, Barry L; Guttman, András

    2009-06-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA-sequencing methods have evolved from the labor-intensive slab gel electrophoresis, through automated multiCE systems using fluorophore labeling with multispectral imaging, to the "next-generation" technologies of cyclic-array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes were only possible with the advent of modern sequencing technologies that were a result of step-by-step advances with a contribution of academics, medical personnel and instrument companies. While next-generation sequencing is moving ahead at breakneck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of CE in DNA sequencing based in part of several of our articles in this journal.

  16. Sequencing the maize genome.

    Science.gov (United States)

    Martienssen, Robert A; Rabinowicz, Pablo D; O'Shaughnessy, Andrew; McCombie, W Richard

    2004-04-01

    Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x coverage of gene-rich regions, accompanied by less than 1x coverage of subclones from BAC contigs, will generate high-quality mapped sequence that meets the needs of geneticists while accommodating unusually high levels of structural polymorphism. By sequencing several inbred strains, we propose a strategy for capturing this polymorphism to investigate hybrid vigor or heterosis.

  17. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    OpenAIRE

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; AKIYAMA, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto seque...

  18. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  19. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  20. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  1. Scope and Sequence.

    Science.gov (United States)

    Callison, Daniel

    2002-01-01

    Discusses scope and sequence plans for curriculum coordination in elementary and secondary education related to school libraries. Highlights include library skills; levels of learning objectives; technology skills; media literacy skills; and information inquiry skills across disciplines by grade level. (LRW)

  2. Evolution of DNA sequencing

    National Research Council Canada - National Science Library

    Tipu, Hamid Nawaz; Shabbir, Ambreen

    2015-01-01

    Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted...

  3. Pierre Robin sequence

    Science.gov (United States)

    Pierre Robin syndrome; Pierre Robin complex; Pierre Robin anomaly ... The exact causes of Pierre Robin sequence are unknown. It may be part of many genetic syndromes. The lower jaw develops slowly before birth, but may grow ...

  4. In Favor of Sequencing?

    NARCIS (Netherlands)

    van der Borgh, G.J.C.

    2014-01-01

    This short article is a contribution to an online discussion about political sequencing and stability. It argues that despite all the risks of democratization in fragile states,a more gradual approach should be preferred.

  5. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  6. Text Mining: (Asynchronous Sequences

    Directory of Open Access Journals (Sweden)

    Sheema Khan

    2014-12-01

    Full Text Available In this paper we tried to correlate text sequences those provides common topics for semantic clues. We propose a two step method for asynchronous text mining. Step one check for the common topics in the sequences and isolates these with their timestamps. Step two takes the topic and tries to give the timestamp of the text document. After multiple repetitions of step two, we could give optimum result.

  7. Malaria Genome Sequencing Project

    Science.gov (United States)

    2004-01-01

    million cases and up to 2.7 million A whole chromosome shotgun sequencing strategy was used to deaths from malaria each year. The mortality levels are...deaths from malaria each year. The mortality levels are greatest in determine the genome sequence of P. falciparum clone 3D7. This sub-Saharan Africa...aminolevulinic acid dehydratase. Cura . Genet. 40, 391-398 (2002). 15. Lasonder, E. et al Analysis of the Plasmodium falciparum proteome by high-accuracy mass

  8. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene......This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis...

  9. Genome sequencing conference II

    Energy Technology Data Exchange (ETDEWEB)

    1990-01-01

    Genome Sequencing Conference 2 was held September 30 to October 30, 1990. 26 speaker abstracts and 33 poster presentations were included in the program report. New and improved methods for DNA sequencing and genetic mapping were presented. Many of the papers were concerned with accuracy and speed of acquisition of data with computers and automation playing an increasing role. Individual papers have been processed separately for inclusion on the database.

  10. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  11. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed Affan

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  12. Controlled processing during sequencing.

    Science.gov (United States)

    Thothathiri, Malathi; Rattinger, Michelle

    2015-01-01

    Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6) in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region's activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  13. Controlled processing during sequencing

    Directory of Open Access Journals (Sweden)

    Malathi eThothathiri

    2015-10-01

    Full Text Available Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6 in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex (ACC. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region’s activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  14. Program Synthesizes UML Sequence Diagrams

    Science.gov (United States)

    Barry, Matthew R.; Osborne, Richard N.

    2006-01-01

    A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

  15. Sequencing BPS Spectra

    CERN Document Server

    Gukov, Sergei; Saberi, Ingmar; Stosic, Marko; Sulkowski, Piotr

    2015-01-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincar\\'e polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular $S$-matrix. This leads to the identifi...

  16. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...

  17. Family Sequencing and Cooperation

    NARCIS (Netherlands)

    Grundel, S.; Ciftci, B.B.; Borm, P.E.M.; Hamers, H.J.M.

    2012-01-01

    To analyze the allocation problem of the maximal cost savings of the whole group of jobs, we define and analyze a so-called corresponding cooperative family sequencing game which explicitly takes into account the maximal cost savings for any coalition of jobs. Using nonstandard techniques we prove t

  18. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak Syst

  19. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  20. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  1. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  2. Rapid-Sequence Intubation

    Directory of Open Access Journals (Sweden)

    Evangelina Dávila Cabo de Villa

    2015-09-01

    Full Text Available In medical practice there are several situations that require immediate intervention of the airway in some patients, in order to ensure proper entrance and exit of gases into and out of the lungs and prevent aspiration. Rapid-sequence intubation has been considered as the administration of a hypnotic agent and a neuromuscular relaxant consecutively (virtually simultaneously to facilitate orotracheal intubation in critically ill patients and minimize the risk of aspiration. This paper aims to collect elements that promote a successful medical management according to the situation presented, since there is no single way of proceeding in case of rapid-sequence intubation. The elements to consider include: knowing the anatomy of the upper respiratory tract, having a group of drugs to choose from, receiving adequate training and having an alternative plan for the difficulties that may arise.

  3. Sequence Classification: 885394 [

    Lifescience Database Archive (English)

    Full Text Available 703); The expression pattern of this gene is described in PMID:12000842; possible frameshift detected when compared...Non-TMB TMH Non-TMB Non-TMB Non-TMB Non-TMB >gi|23619146|ref|NP_705108.1| Slight di...fference exist when compared to the published sequence of EBL-1 from Dd2 strain of P. falciparum (PMID:10613

  4. Sequencing of aromatase inhibitors

    OpenAIRE

    2005-01-01

    Since the development of the third-generation aromatase inhibitors (AIs), anastrozole, letrozole and exemestane, these agents have been the subject of intensive research to determine their optimal use in advanced breast cancer. Not only have they replaced progestins in second-line therapy and challenged the role of tamoxifen in first-line, but there is also evidence for a lack of cross-resistance between the steroidal and nonsteroidal AIs, meaning that they may be used in sequence to obtain p...

  5. Properties of Semijoin Sequences

    Institute of Scientific and Technical Information of China (English)

    BengC.Ooi; B.Srinivasan

    1989-01-01

    The problem of finding optimum semijoin sequ4ence of an arbitrary query under linear cost function for the transmission cost is NP.hard.Hence heuristic algorithms with desirable properties are explored.In this paper four properties of semijoin programs for distributed query processing are identified,The use of these properties in constructing semijoin sequence is justified.An existing algorithm is modified incorporating these properties.Empirical comparison with existing algorithms shows the superiority of the proposed algorithm.

  6. Learning Sequence Neighbourhood Metrics

    CERN Document Server

    Bayer, Justin; van der Smagt, Patrick

    2011-01-01

    Recurrent neural networks (RNNs) in combination with a pooling operator and the neighbourhood components analysis (NCA) objective function are able to detect the characterizing dynamics of sequences and embed them into a fixed-length vector space of arbitrary dimensionality. Subsequently, the resulting features are meaningful and can be used for visualization or nearest neighbour classification in linear time. This kind of metric learning for sequential data enables the use of algorithms tailored towards fixed length vector spaces such as R^n.

  7. Sequencing BPS spectra

    Science.gov (United States)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-03-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d {N}=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  8. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  9. The Galaxy End Sequence

    Science.gov (United States)

    Eales, Stephen; de Vis, Pieter; Smith, Matthew W. L.; Appah, Kiran; Ciesla, Laure; Duffield, Chris; Schofield, Simon

    2017-03-01

    A common assumption is that galaxies fall in two distinct regions of a plot of specific star formation rate (SSFR) versus galaxy stellar mass: a star-forming galaxy main sequence (GMS) and a separate region of 'passive' or 'red and dead galaxies'. Starting from a volume-limited sample of nearby galaxies designed to contain most of the stellar mass in this volume, and thus representing the end-point of ≃12 billion years of galaxy evolution, we investigate the distribution of galaxies in this diagram today. We show that galaxies follow a strongly curved extended GMS with a steep negative slope at high galaxy stellar masses. There is a gradual change in the morphologies of the galaxies along this distribution, but there is no clear break between early-type and late-type galaxies. Examining the other evidence that there are two distinct populations, we argue that the 'red sequence' is the result of the colours of galaxies changing very little below a critical value of the SSFR, rather than implying a distinct population of galaxies. Herschel observations, which show at least half of early-type galaxies contain a cool interstellar medium, also imply continuity between early-type and late-type galaxies. This picture of a unitary population of galaxies requires more gradual evolutionary processes than the rapid quenching process needed to explain two distinct populations. We challenge theorists to predict quantitatively the properties of this 'Galaxy End Sequence'.

  10. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  11. Information Theory of DNA Sequencing

    CERN Document Server

    Motahari, Abolfazl; Tse, David

    2012-01-01

    DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. By drawing an analogy between the DNA sequencing problem and the classic communication problem, we define an information theoretic notion of sequencing capacity. This is the maximum number of DNA base pairs that can be resolved reliably per read, and provides a fundamental limit to the performance that can be achieved by any assembly algorithm. We compute the sequencing capacity explicitly for a simple statistical model of the DNA sequence and the read process. Using this framework, we also study the impact of noise in the read process on the sequencing capacity.

  12. A vision for ubiquitous sequencing.

    Science.gov (United States)

    Erlich, Yaniv

    2015-10-01

    Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors--miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors.

  13. Psychoacoustic Properties of Fibonacci Sequences

    Directory of Open Access Journals (Sweden)

    J. Sokoll

    2008-01-01

    Full Text Available 1202, Fibonacci set up one of the most interesting sequences in number theory. This sequence can be represented by so-called Fibonacci Numbers, and by a binary sequence of zeros and ones. If such a binary Fibonacci Sequence is played back as an audio file, a very dissonant sound results. This is caused by the “almost-periodic”, “self-similar” property of the binary sequence. The ratio of zeros and ones converges to the golden ratio, as do the primary and secondary spectral components intheir frequencies and amplitudes. These Fibonacci Sequences will be characterized using listening tests and psychoacoustic analyses. 

  14. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad

    1956-01-01

    One of the finest expositors in the field of modern mathematics, Dr. Konrad Knopp here concentrates on a topic that is of particular interest to 20th-century mathematicians and students. He develops the theory of infinite sequences and series from its beginnings to a point where the reader will be in a position to investigate more advanced stages on his own. The foundations of the theory are therefore presented with special care, while the developmental aspects are limited by the scope and purpose of the book. All definitions are clearly stated; all theorems are proved with enough detail to ma

  15. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  16. Spaces of Ideal Convergent Sequences

    Directory of Open Access Journals (Sweden)

    M. Mursaleen

    2014-01-01

    Full Text Available In the present paper, we introduce some sequence spaces using ideal convergence and Musielak-Orlicz function ℳ=Mk. We also examine some topological properties of the resulting sequence spaces.

  17. Sequence Handling by Sequence Analysis Toolbox v1.0

    DEFF Research Database (Denmark)

    Ingrell, Christian Ravnsborg; Matthiesen, Rune; Jensen, Ole Nørregaard

    2006-01-01

    The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence...... analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl...

  18. The Galaxy End Sequence

    CERN Document Server

    Eales, Stephen; Smith, Matthew; Appah, Kiran; Ciesla, Laure; Duffield, Chris; Schofield, Simon

    2016-01-01

    A common assumption is that galaxies fall in two distinct regions on a plot of specific star-formation rate (SSFR) versus galaxy stellar mass: a star-forming Galaxy Main Sequence (GMS) and a separate region of `passive' or `red and dead galaxies'. Starting from a volume-limited sample of nearby galaxies designed to contain most of the stellar mass in this volume, and thus being a fair representation of the Universe at the end of 12 billion years of galaxy evolution, we investigate the distribution of galaxies in this diagram today. We show that galaxies follow a strongly curved extended GMS with a steep negative slope at high galaxy stellar masses. There is a gradual change in the morphologies of the galaxies along this distribution, but there is no clear break between early-type and late-type galaxies. Examining the other evidence that there are two distinct populations, we argue that the `red sequence' is the result of the colours of galaxies changing very little below a critical value of the SSFR, rather t...

  19. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  20. Novel sequences propel familiar folds.

    Science.gov (United States)

    Jawad, Zahra; Paoli, Massimo

    2002-04-01

    Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.

  1. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS...... the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56...... MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types...

  2. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    Science.gov (United States)

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; Akiyama, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin; Hazama, Makoto; Nishine, Tsutomu; Harada, Akira; Yamamoto, Rintaro; Matsumoto, Hiroyuki; Sakaguchi, Sumito; Ikegami, Takashi; Kashiwagi, Katsuya; Fujiwake, Syuji; Inoue, Kouji; Togawa, Yoshiyuki; Izawa, Masaki; Ohara, Eiji; Watahiki, Masanori; Yoneda, Yuko; Ishikawa, Tomokazu; Ozawa, Kaori; Tanaka, Takumi; Matsuura, Shuji; Kawai, Jun; Okazaki, Yasushi; Muramatsu, Masami; Inoue, Yorinao; Kira, Akira; Hayashizaki, Yoshihide

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3′ end and 5′ end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can

  3. RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer.

    Science.gov (United States)

    Shibata, K; Itoh, M; Aizawa, K; Nagaoka, S; Sasaki, N; Carninci, P; Konno, H; Akiyama, J; Nishi, K; Kitsunai, T; Tashiro, H; Itoh, M; Sumi, N; Ishii, Y; Nakamura, S; Hazama, M; Nishine, T; Harada, A; Yamamoto, R; Matsumoto, H; Sakaguchi, S; Ikegami, T; Kashiwagi, K; Fujiwake, S; Inoue, K; Togawa, Y

    2000-11-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3' end and 5' end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be

  4. Musical Sequences in Comics

    Directory of Open Access Journals (Sweden)

    Kieron Michael Brown

    2013-11-01

    Full Text Available Critical attention paid to the media of music and comics has historically focused on parallels between the temporal rhythm and pacing of music and the implied rhythm and temporality of comics (Eisner 2008, Godek 2007. Recent attention has begun to focus on both comics’ potential to represent the character of music (Whitted 2011 and the effects of musical images and themes on comics’ narratology (Peters 2013.    I suggest that analyses of comics that combine the traditional interplay of image and word with the use of elements of musical notation are able to shed further light on each of these areas, via the connotations and conventions of symbols pulled exclusively from the realms of music, and their integration with the other elements of the page in sequence.

  5. Solid phase sequencing of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles (Del Mar, CA); Koster, Hubert (La Jolla, CA)

    2010-09-28

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  6. Computer processing sleep data of two-channel electroencephalogram and one-channel electrooculogram by aperiodic waveform analysis%计算机处理睡眠数据中2导脑电和1导眼电的非周期波形分析

    Institute of Scientific and Technical Information of China (English)

    王国锋; 彭小虎

    2011-01-01

    BACKGROUND: The sleep data are very large, and it is not satisfied with practice demand if the data cannot process by computer However, the methods which are using at present have a disadvantage that the accuracy is comparatively low OBJECTIVE: To investigate a new method for sleep stage classification only using electroencephalogram (EEG) and electrooculogram (EOG) based on aperiodic waveform analysis and genetic neural network of radial basis function (RBF) METHODS: Raw data including two-channel EEG and one-channel EOG recorded from eight subjects were obtained from Sleep-EDF database of PhysioBank, MIT After digital filter with zero phase, raw data were analyzed by aperiodic waveform analysis to extract several parameters that were necessary for sleep stage classification Then, preprocessed data as input for genetic neural network of RBF accepted training Finally, test data were sent to trained neural network to validate RESULTS AND CONCLUSION: The results obtained, on average 95 6% of agreement between the expert and the GA-ANN for six stages of vigilance, going beyond results of known literature (70%-90%), which possess high value in practice and maybe satisfy with research and clinical application%背景:睡眠中记录的数据量很大,不用计算机自动处理不能满足实用需要,而现有的对睡眠数据进行分期的方法准确率都不高.目的:考察仅依据脑电与眼电,基于非周期波形分析和径向基函数遗传神经网络的睡眠数据分期新方法.方法:实验数据来自MIT的PhysioBank中的S1eep-EDF数据库,共8名被试,各记录2导脑电和1导眼电.原始数据经零相位数字滤波后,进行非周期波形分析,得出每个Epoch的特征向量,经预处理后送遗传径向基函数.神经网络配合专家手工分类结果进行训练,训练好的神经网络再对测试数据进行分析.结果与结论:总的分期符合率为95.6%,超出已知文献研究结果(70%~90%),具有很高的实用价值,

  7. Solid phase sequencing of biopolymers

    Science.gov (United States)

    Cantor, Charles R.; Hubert, Koster

    2014-06-24

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Probes may be affixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  8. Graphene nanodevices for DNA sequencing

    Science.gov (United States)

    Heerema, Stephanie J.; Dekker, Cees

    2016-02-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

  9. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  10. Nonlinear analysis of biological sequences

    Energy Technology Data Exchange (ETDEWEB)

    Torney, D.C.; Bruno, W.; Detours, V. [and others

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The main objectives of this project involved deriving new capabilities for analyzing biological sequences. The authors focused on tabulating the statistical properties exhibited by Human coding DNA sequences and on techniques of inferring the phylogenetic relationships among protein sequences related by descent.

  11. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  12. Blazar Sequence in Fermi Era

    Indian Academy of Sciences (India)

    Liang Chen

    2014-09-01

    In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power-high-synchrotron-peaked and low-power-low-sychrotron-peaked blazars. Because most blazars have similar size of emission region, theoretical blazar sequence implies that the break of Spectral Energy Distribution (SED) is a cooling break in nature.

  13. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  14. Assembly sequencing with toleranced parts

    Energy Technology Data Exchange (ETDEWEB)

    Latombe, J.C. [Stanford Univ., CA (United States). Robotics Lab.; Wilson, R.H. [Sandia National Labs., Albuquerque, NM (United States). Intelligent Systems and Robotics Center

    1995-02-21

    The goal of assembly sequencing is to plan a feasible series of operations to construct a product from its individual parts. Previous research has thoroughly investigated assembly sequencing under the assumption that parts have nominal geometry. This paper considers the case where parts have toleranced geometry. Its main contribution is an efficient procedure that decides if a product admits an assembly sequence with infinite translations that is feasible for all possible instances of the components within the specified tolerances. If the product admits one such sequence, the procedure can also generate it. For the cases where there exists no such assembly sequence, another procedure is proposed which generates assembly sequences that are feasible only for some values of the toleranced dimensions. If this procedure produces no such sequence, then no instance of the product is assemblable. Finally, this paper analyzes the relation between assembly and disassembly sequences in the presence of toleranced parts. This work assumes a simple, but non-trivial tolerance language that falls short of capturing all imperfections of a manufacturing process. Hence, it is only one step toward assembly sequencing with toleranced parts.

  15. SNMR pulse sequence phase cycling

    Science.gov (United States)

    Walsh, David O; Grunewald, Elliot D

    2013-11-12

    Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

  16. The ontology of biological sequences

    Directory of Open Access Journals (Sweden)

    Kelso Janet

    2009-11-01

    Full Text Available Abstract Background Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most basic question about sequences remains unanswered: what kind of entity is a biological sequence? An answer to this question benefits formal ontologies that use the notion of biological sequences and analyses in computational biology alike. Results We provide both an ontological analysis of biological sequences and a formal representation that can be used in knowledge-based applications and other ontologies. We distinguish three distinct kinds of entities that can be referred to as "biological sequence": chains of molecules, syntactic representations such as those in biological databases, and the abstract information-bearing entities. For use in knowledge-based applications and inclusion in biomedical ontologies, we implemented the developed axiom system for use in automated theorem proving. Conclusion Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications.

  17. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  18. Sequence Algebra, Sequence Decision Diagrams and Dynamic Fault Trees

    Energy Technology Data Exchange (ETDEWEB)

    Rauzy, Antoine B., E-mail: Antoine.Rauzy@lix.polytechnique.f [LIX-CNRS, Computer Science, Ecole Polytechnique, 91128 Palaiseau Cedex (France)

    2011-07-15

    A large attention has been focused on the Dynamic Fault Trees in the past few years. By adding new gates to static (regular) Fault Trees, Dynamic Fault Trees aim to take into account dependencies among events. Merle et al. proposed recently an algebraic framework to give a formal interpretation to these gates. In this article, we extend Merle et al.'s work by adopting a slightly different perspective. We introduce Sequence Algebras that can be seen as Algebras of Basic Events, representing failures of non-repairable components. We show how to interpret Dynamic Fault Trees within this framework. Finally, we propose a new data structure to encode sets of sequences of Basic Events: Sequence Decision Diagrams. Sequence Decision Diagrams are very much inspired from Minato's Zero-Suppressed Binary Decision Diagrams. We show that all operations of Sequence Algebras can be performed on this data structure.

  19. NSIT: novel sequence identification tool.

    Directory of Open Access Journals (Sweden)

    Benjarath Pupacdi

    Full Text Available Novel sequences are DNA sequences present in an individual's genome but absent in the human reference assembly. They are predicted to be biologically important, both individual and population specific, and consistent with the known human migration paths. Recent works have shown that an average person harbors 2-5 Mb of such sequences and estimated that the human pan-genome contains as high as 19-40 Mb of novel sequences. To identify them in a de novo genome assembly, some existing sequence aligners have been used but no computational method has been specifically proposed for this task. In this work, we developed NSIT (Novel Sequence Identification Tool, a software that can accurately and efficiently identify novel sequences in an individual's de novo whole genome assembly. We identified and characterized 1.1 Mb, 1.2 Mb, and 1.0 Mb of novel sequences in NA18507 (African, YH (Asian, and NA12878 (European de novo genome assemblies, respectively. Our results show very high concordance with the previous work using the respective reference assembly. In addition, our results using the latest human reference assembly suggest that the amount of novel sequences per individual may not be as high as previously reported. We additionally developed a graphical viewer for comparisons of novel sequence contents. The viewer also helped in identifying sequence contamination; we found 130 kb of Epstein-Barr virus sequence in the previously published NA18507 novel sequences as well as 287 kb of zebrafish repeats in NA12878 de novo assembly. NSIT requires [Formula: see text]2GB of RAM and 1.5-2 hrs on a commodity desktop. The program is applicable to input assemblies with varying contig/scaffold sizes, ranging from 100 bp to as high as 50 Mb. It works in both 32-bit and 64-bit systems and outperforms, by large margins, other fast sequence aligners previously applied to this task. To our knowledge, NSIT is the first software designed specifically for novel sequence

  20. PERIODIC COMPLEMENTARY BINARY SEQUENCE PAIRS

    Institute of Scientific and Technical Information of China (English)

    XuChengqian; ZhaoXiaoqun

    2002-01-01

    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP)is proposed .A new class of block design-Difference Family Pair (DFP)is also proposed .The relationship between PCSP and DFP,the properties and exising conditions of PCSP and the recursive constructions for PCSP are given.

  1. PERIODIC COMPLEMENTARY BINARY SEQUENCE PAIRS

    Institute of Scientific and Technical Information of China (English)

    Xu Chengqian; Zhao Xiaoqun

    2002-01-01

    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP) is proposed. A new class of block design-Difference Family Pair (DFP) is also proposed.The relationship between PCSP and DFP, the properties and existing conditions of PCSP and the recursive constructions for PCSP are given.

  2. DNA Sequencing Sensors: An Overview

    Directory of Open Access Journals (Sweden)

    Jose Antonio Garrido-Cardenas

    2017-03-01

    Full Text Available The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger. The emergence of mass sequencing sensors, or new generation sequencing (NGS meant a quantitative leap both in the volume of genetic material that was able to be sequenced in each trial, as well as in the time per run and its cost. One can envisage that incoming technologies, already known as fourth generation sequencing, will continue to cheapen the trials by increasing DNA reading lengths in each run. All of this would be impossible without sensors and detection systems becoming smaller and more precise. This article provides a comprehensive overview on sensors for DNA sequencing developed within the last 40 years.

  3. Gambling strategies for random sequences

    OpenAIRE

    George Davie

    2010-01-01

    There is a general consensus that it is not possible to gamble successfully against a random se-quence. This consensus is based on results from probability theory that all gambling systems arein some sense futile and the idea that at any stage of the sequence, the next outcome is entirelyunpredictable.

  4. Sequence conserved for subcellular localization

    Science.gov (United States)

    Nair, Rajesh; Rost, Burkhard

    2002-01-01

    The more proteins diverged in sequence, the more difficult it becomes for bioinformatics to infer similarities of protein function and structure from sequence. The precise thresholds used in automated genome annotations depend on the particular aspect of protein function transferred by homology. Here, we presented the first large-scale analysis of the relation between sequence similarity and identity in subcellular localization. Three results stood out: (1) The subcellular compartment is generally more conserved than what might have been expected given that short sequence motifs like nuclear localization signals can alter the native compartment; (2) the sequence conservation of localization is similar between different compartments; and (3) it is similar to the conservation of structure and enzymatic activity. In particular, we found the transition between the regions of conserved and nonconserved localization to be very sharp, although the thresholds for conservation were less well defined than for structure and enzymatic activity. We found that a simple measure for sequence similarity accounting for pairwise sequence identity and alignment length, the HSSP distance, distinguished accurately between protein pairs of identical and different localizations. In fact, BLAST expectation values outperformed the HSSP distance only for alignments in the subtwilight zone. We succeeded in slightly improving the accuracy of inferring localization through homology by fine tuning the thresholds. Finally, we applied our results to the entire SWISS-PROT database and five entirely sequenced eukaryotes. PMID:12441382

  5. Bayesian analysis of binary sequences

    Science.gov (United States)

    Torney, David C.

    2005-03-01

    This manuscript details Bayesian methodology for "learning by example", with binary n-sequences encoding the objects under consideration. Priors prove influential; conformable priors are described. Laplace approximation of Bayes integrals yields posterior likelihoods for all n-sequences. This involves the optimization of a definite function over a convex domain--efficiently effectuated by the sequential application of the quadratic program.

  6. Chameleon sequences in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  7. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  8. Spatiotemporal correlations of aftershock sequences

    CERN Document Server

    Peixoto, Tiago P; Davidsen, Jörn

    2010-01-01

    Aftershock sequences are of particular interest in seismic research since they may condition seismic activity in a given region over long time spans. While they are typically identified with periods of enhanced seismic activity after a large earthquake as characterized by the Omori law, our knowledge of the spatiotemporal correlations between events in an aftershock sequence is limited. Here, we study the spatiotemporal correlations of two aftershock sequences form California (Parkfield and Hector Mine) using the recently introduced concept of "recurrent" events. We find that both sequences have very similar properties and that most of them are captured by the space-time epidemic-type aftershock sequence (ETAS) model if one takes into account catalog incompleteness. However, the stochastic model does not capture the spatiotemporal correlations leading to the observed structure of seismicity on small spatial scales.

  9. Quantum Exchangeable Sequences of Algebras

    CERN Document Server

    Curran, Stephen

    2008-01-01

    We extend the notion of quantum exchangeability, introduced by K\\"ostler and Speicher in arXiv:0807.0677, to sequences (\\rho_1,\\rho_2,...c) of homomorphisms from an algebra C into a noncommutative probability space (A,\\phi), and prove a free de Finetti theorem: an infinite quantum exchangeable sequence (\\rho_1,\\rho_2,...c) is freely independent and identically distributed with respect to a conditional expectation. As a corollary we obtain a free analogue of the Hewitt Savage zero-one law. As in the classical case, the theorem fails for finite sequences. We give a characterization of finite quantum exchangeable sequences, which can be viewed as a noncommutative analogue of sampling without replacement. We then give an approximation to how far a finite quantum exchangeable sequence is from being freely independent with amalgamation.

  10. Ossification sequence heterochrony among amphibians.

    Science.gov (United States)

    Harrington, Sean M; Harrison, Luke B; Sheil, Christopher A

    2013-01-01

    Heterochrony is an important mechanism in the evolution of amphibians. Although studies have centered on the relationship between size and shape and the rates of development, ossification sequence heterochrony also may have been important. Rigorous, phylogenetic methods for assessing sequence heterochrony are relatively new, and a comprehensive study of the relative timing of ossification of skeletal elements has not been used to identify instances of sequence heterochrony across Amphibia. In this study, a new version of the program Parsimov-based genetic inference (PGi) was used to identify shifts in ossification sequences across all extant orders of amphibians, for all major structural units of the skeleton. PGi identified a number of heterochronic sequence shifts in all analyses, the most interesting of which seem to be tied to differences in metamorphic patterns among major clades. Early ossification of the vomer, premaxilla, and dentary is retained by Apateon caducus and members of Gymnophiona and Urodela, which lack the strongly biphasic development seen in anurans. In contrast, bones associated with the jaws and face were identified as shifting late in the ancestor of Anura. The bones that do not shift late, and thereby occupy the earliest positions in the anuran cranial sequence, are those in regions of the skull that undergo the least restructuring throughout anuran metamorphosis. Additionally, within Anura, bones of the hind limb and pelvic girdle were also identified as shifting early in the sequence of ossification, which may be a result of functional constraints imposed by the drastic metamorphosis of most anurans.

  11. A Criterion for Regular Sequences

    Indian Academy of Sciences (India)

    D P Patil; U Storch; J Stückrad

    2004-05-01

    Let be a commutative noetherian ring and $f_1,\\ldots,f_r \\in R$. In this article we give (cf. the Theorem in $\\mathcal{x}$2) a criterion for $f_1,\\ldots,f_r$ to be regular sequence for a finitely generated module over which strengthens and generalises a result in [2]. As an immediate consequence we deduce that if $V(g_1,\\ldots,g_r) \\subseteq V(f_1,\\ldots,f_r)$ in Spec and if $f_1,\\ldots,f_r$ is a regular sequence in , then $g_1,\\ldots,g_r$ is also a regular sequence in .

  12. Weak disorder in Fibonacci sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Naim, E [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Krapivsky, P L [Department of Physics and Center for Molecular Cybernetics, Boston University, Boston, MA 02215 (United States)

    2006-05-19

    We study how weak disorder affects the growth of the Fibonacci series. We introduce a family of stochastic sequences that grow by the normal Fibonacci recursion with probability 1 - {epsilon}, but follow a different recursion rule with a small probability {epsilon}. We focus on the weak disorder limit and obtain the Lyapunov exponent that characterizes the typical growth of the sequence elements, using perturbation theory. The limiting distribution for the ratio of consecutive sequence elements is obtained as well. A number of variations to the basic Fibonacci recursion including shift, doubling and copying are considered. (letter to the editor)

  13. ISIS Individualized Support In Sequencing

    NARCIS (Netherlands)

    Drachsler, Hendrik; Hummel, Hans

    2007-01-01

    Drachsler, H., & Hummel, H. G. K. (2007). ISIS Individualized Support In Sequencing. Presentation given during the PIP meeting on March 22, 2007. Open University of the Netherlands: Heerlen, The Netherlands.

  14. Molecular beacon sequence design algorithm.

    Science.gov (United States)

    Monroe, W Todd; Haselton, Frederick R

    2003-01-01

    A method based on Web-based tools is presented to design optimally functioning molecular beacons. Molecular beacons, fluorogenic hybridization probes, are a powerful tool for the rapid and specific detection of a particular nucleic acid sequence. However, their synthesis costs can be considerable. Since molecular beacon performance is based on its sequence, it is imperative to rationally design an optimal sequence before synthesis. The algorithm presented here uses simple Microsoft Excel formulas and macros to rank candidate sequences. This analysis is carried out using mfold structural predictions along with other free Web-based tools. For smaller laboratories where molecular beacons are not the focus of research, the public domain algorithm described here may be usefully employed to aid in molecular beacon design.

  15. Classification of Base Sequences (+1,

    Directory of Open Access Journals (Sweden)

    Dragomir Ž. Ðoković

    2010-01-01

    Full Text Available Base sequences BS(+1, are quadruples of {±1}-sequences (;;;, with A and B of length +1 and C and D of length n, such that the sum of their nonperiodic autocor-relation functions is a -function. The base sequence conjecture, asserting that BS(+1, exist for all n, is stronger than the famous Hadamard matrix conjecture. We introduce a new definition of equivalence for base sequences BS(+1, and construct a canonical form. By using this canonical form, we have enumerated the equivalence classes of BS(+1, for ≤30. As the number of equivalence classes grows rapidly (but not monotonically with n, the tables in the paper cover only the cases ≤13.

  16. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  17. Pythagorean Triples from Harmonic Sequences.

    Science.gov (United States)

    DiDomenico, Angelo S.; Tanner, Randy J.

    2001-01-01

    Shows how all primitive Pythagorean triples can be generated from harmonic sequences. Use inductive and deductive reasoning to explore how Pythagorean triples are connected with another area of mathematics. (KHR)

  18. Overview of Sequence Data Formats.

    Science.gov (United States)

    Zhang, Hongen

    2016-01-01

    Next-generation sequencing experiment can generate billions of short reads for each sample and processing of the raw reads will add more information. Various file formats have been introduced/developed in order to store and manipulate this information. This chapter presents an overview of the file formats including FASTQ, FASTA, SAM/BAM, GFF/GTF, BED, and VCF that are commonly used in analysis of next-generation sequencing data.

  19. Structural Complexity of DNA Sequence

    Directory of Open Access Journals (Sweden)

    Cheng-Yuan Liou

    2013-01-01

    Full Text Available In modern bioinformatics, finding an efficient way to allocate sequence fragments with biological functions is an important issue. This paper presents a structural approach based on context-free grammars extracted from original DNA or protein sequences. This approach is radically different from all those statistical methods. Furthermore, this approach is compared with a topological entropy-based method for consistency and difference of the complexity results.

  20. Nanogrid rolling circle DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Church, George M.; Porreca, Gregory J.; Shendure, Jay; Rosenbaum, Abraham Meir

    2017-04-18

    The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer.

  1. Pig genome sequence - analysis and publication strategy

    NARCIS (Netherlands)

    Archibald, A.L.; Bolund, L.; Churcher, C.; Fredholm, M.; Groenen, M.A.M.; Harlizius, B.

    2010-01-01

    Background - The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing. Results - Assemblies of the B

  2. Long-range barcode labeling-sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Feng; Zhang, Tao; Singh, Kanwar K.; Pennacchio, Len A.; Froula, Jeff L.; Eng, Kevin S.

    2016-10-18

    Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

  3. Sequencing and comparative analysis of the gorilla MHC genomic sequence.

    Science.gov (United States)

    Wilming, Laurens G; Hart, Elizabeth A; Coggill, Penny C; Horton, Roger; Gilbert, James G R; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David; Beck, Stephan; Harrow, Jennifer L

    2013-01-01

    Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC.

  4. Synchronization of cardiorhythm by weak external forcing

    Directory of Open Access Journals (Sweden)

    V. S. Anishchenko

    2000-01-01

    Full Text Available We study the possibility to synchronize cardiorhythm of a human by periodic and aperiodic sequences of light and sound pulses. Aperiodic forcing is defined by variation of RR intervals of another subject. Phase locking between cardiorhythm and weak external forcing is detected on finite time intervals. We observe the 1:1 synchronization for periodic forcing and n:m synchronization for aperiodic one.

  5. ARC Code TI: sequenceMiner

    Data.gov (United States)

    National Aeronautics and Space Administration — The sequenceMiner was developed to address the problem of detecting and describing anomalies in large sets of high-dimensional symbol sequences. sequenceMiner works...

  6. Sequencing Needs for Viral Diagnostics

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S N; Lam, M; Mulakken, N J; Torres, C L; Smith, J R; Slezak, T

    2004-01-26

    We built a system to guide decisions regarding the amount of genomic sequencing required to develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify a viral species. We used our existing DNA diagnostic signature prediction pipeline, which selects regions of a target species genome that are conserved among strains of the target (for reliability, to prevent false negatives) and unique relative to other species (for specificity, to avoid false positives). We performed simulations, based on existing sequence data, to assess the number of genome sequences of a target species and of close phylogenetic relatives (''near neighbors'') that are required to predict diagnostic signature regions that are conserved among strains of the target species and unique relative to other bacterial and viral species. For DNA viruses such as variola (smallpox), three target genomes provide sufficient guidance for selecting species-wide signatures. Three near neighbor genomes are critical for species specificity. In contrast, most RNA viruses require four target genomes and no near neighbor genomes, since lack of conservation among strains is more limiting than uniqueness. SARS and Ebola Zaire are exceptional, as additional target genomes currently do not improve predictions, but near neighbor sequences are urgently needed. Our results also indicate that double stranded DNA viruses are more conserved among strains than are RNA viruses, since in most cases there was at least one conserved signature candidate for the DNA viruses and zero conserved signature candidates for the RNA viruses.

  7. Sequence-dependent nucleosome positioning.

    Science.gov (United States)

    Chung, Ho-Ryun; Vingron, Martin

    2009-03-13

    Eukaryotic DNA is organized into a macromolecular structure called chromatin. The basic repeating unit of chromatin is the nucleosome, which consists of two copies of each of the four core histones and DNA. The nucleosomal organization and the positions of nucleosomes have profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is therefore of general interest. Among the many determinants of nucleosome positioning, the DNA sequence has been proposed to have a major role. Here, we analyzed more than 860,000 nucleosomal DNA sequences to identify sequence features that guide the formation of nucleosomes in vivo. We found that both a periodic enrichment of AT base pairs and an out-of-phase oscillating enrichment of GC base pairs as well as the overall preference for GC base pairs are determinants of nucleosome positioning. The preference for GC pairs can be related to a lower energetic cost required for deformation of the DNA to wrap around the histones. In line with this idea, we found that only incorporation of both signal components into a sequence model for nucleosome formation results in maximal predictive performance on a genome-wide scale. In this manner, one achieves greater predictive power than published approaches. Our results confirm the hypothesis that the DNA sequence has a major role in nucleosome positioning in vivo.

  8. Explaining the harmonic sequence paradox.

    Science.gov (United States)

    Schmidt, Ulrich; Zimper, Alexander

    2012-05-01

    According to the harmonic sequence paradox, an expected utility decision maker's willingness to pay for a gamble whose expected payoffs evolve according to the harmonic series is finite if and only if his marginal utility of additional income becomes zero for rather low payoff levels. Since the assumption of zero marginal utility is implausible for finite payoff levels, expected utility theory - as well as its standard generalizations such as cumulative prospect theory - are apparently unable to explain a finite willingness to pay. This paper presents first an experimental study of the harmonic sequence paradox. Additionally, it demonstrates that the theoretical argument of the harmonic sequence paradox only applies to time-patient decision makers, whereas the paradox is easily avoided if time-impatience is introduced.

  9. Transgressive Surface as Sequence Boundary

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Analysis of the four cases of the sequence boundary (SB)-transgressive surface (TS) relation in nature shows that applying transgressive surfaces as sequence boundaries has the following merits: it improves the methodology of stratigraphic subdivision; the position of transgressive surface in a sea level curve is relatively fixed; the transgressive surface is a transforming surface of the stratal structure; in platforms or ramps, the transgressive surface is the only choice for determining the sequence boundary; the transgressive surface is a readily recognized physical surface reflected by seismic records in seismostratigraphy. The paper reaches a conclusion that to delineate a SB in terms of the TS is theoretically and practically better than to delineate it between highstand and lowstand sediments as has been done traditionally.

  10. On the base sequence conjecture

    CERN Document Server

    Djokovic, Dragomir Z

    2010-01-01

    Let BS(m,n) denote the set of base sequences (A;B;C;D), with A and B of length m and C and D of length n. The base sequence conjecture (BSC) asserts that BS(n+1,n) exist (i.e., are non-empty) for all n. This is known to be true for n <= 36 and when n is a Golay number. We show that it is also true for n=37 and n=38. It is worth pointing out that BSC is stronger than the famous Hadamard matrix conjecture. In order to demonstrate the abundance of base sequences, we have previously attached to BS(n+1,n) a graph Gamma_n and computed the Gamma_n for n <= 27. We now extend these computations and determine the Gamma_n for n=28,...,35. We also propose a conjecture describing these graphs in general.

  11. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    . All but one sequence mapped to the MCP gene while the last sequence mapped to the Neurofilament gene. Approx. half of the sequences contained no errors while the rest differed with 88-99 percent similarity with most having 99% similarity. One sequence, when BLASTed, showed most similarity to European...... Sheatfish and not EHNV. Generally, mistakes occurred at the ends of the sequences. This can be due to several factors. One is that the sequence has not been trimmed of the sequence primer sites. Another is the lack of quality control of the chromatogram. Finally, sequencing in just one direction can result...

  12. Sequence Patterns of Identity Authentication Protocols

    Institute of Scientific and Technical Information of China (English)

    Tao Hongcai; He Dake

    2006-01-01

    From the viewpoint of protocol sequence, analyses are made of the sequence patterns of possible identity authentication protocol under two cases: with or without the trusted third party (TTP). Ten feasible sequence patterns of authentication protocol with TTP and 5 sequence patterns without TTP are gained. These gained sequence patterns meet the requirements for identity authentication,and basically cover almost all the authentication protocols with TTP and without TTP at present. All of the sequence patterns gained are classified into unilateral or bilateral authentication. Then , according to the sequence symmetry, several good sequence patterns with TTP are evaluated. The accompolished results can provide a reference to design of new identity authentication protocols.

  13. KERNEL WORDS AND GAP SEQUENCE OF THE TRIBONACCI SEQUENCE

    Institute of Scientific and Technical Information of China (English)

    Yuke HUANG; Zhiying WEN

    2016-01-01

    In this paper, we investigate the factor properties and gap sequence of the Tri-bonacci sequence, the fixed point of the substitution σ(a, b, c) = (ab, ac, a). Let ωp be the p-th occurrence of ω and Gp(ω) be the gap between ωp and ωp+1. We introduce a notion of kernel for each factor ω, and then give the decomposition of the factor ω with respect to its kernel. Using the kernel and the decomposition, we prove the main result of this paper:for each factorω, the gap sequence{Gp(ω)}p≥1 is the Tribonacci sequence over the alphabet{G1(ω), G2(ω), G4(ω)}, and the expressions of gaps are determined completely. As an appli-cation, for each factorω and p∈N, we determine the position ofωp. Finally we introduce a notion of spectrum for studying some typical combinatorial properties, such as power, overlap and separate of factors.

  14. Sequences and series involving the sequence of composite numbers

    Directory of Open Access Journals (Sweden)

    Panayiotis Vlamos

    2002-01-01

    Full Text Available Denoting by pn and cn the nth prime number and the nth composite number, respectively, we prove that both the sequence (xnn≥1, defined by xn=∑k=1n (ck+1−ck / k−pn / n, and the series ∑n=1∞ (pcn−cpn / npn are convergent.

  15. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P

    1998-02-01

    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  16. Network motifs in music sequences

    CERN Document Server

    Zanette, Damian H

    2010-01-01

    In this note, I summarize ongoing research on motif distribution in networks built up out of symbolic sequences of Western musical origin. Their motif significance profiles exhibit remarkable consistency over different styles and periods, and define a class that cannot be identified with any of the four "superfamilies" to which most real networks seem to belong. Networks from music sequences possess an unusual abundance of bidirectional connections, due to the inherent reversibility of short musical note patterns. This property contributes to motif significance from both local and large-scale features of musical structure.

  17. Convergence of Fuzzy Set Sequences

    Institute of Scientific and Technical Information of China (English)

    FENG Yu-hu

    2002-01-01

    There are more than one mode of convergence with respect to the fuzzy set sequences. In this paper,common six modes of convergence and their relationships are discussed. These six modes are convergence in uniform metric D, convergence in separable metric Dp or D*p, 1 ≤ p <∞, convergence in level set, strong convergence in level set and weak convergence. Suitable counterexamples are given. The necessary and sufficient conditions of convergence in uniform metric D are described. Some comme nts on the convergence of LRfuzzy number sequences are represented.

  18. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  19. The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Toon Rosseel

    Full Text Available Sequence Independent Single Primer Amplification is one of the most widely used random amplification approaches in virology for sequencing template preparation. This technique relies on oligonucleotides consisting of a 3' random part used to prime complementary DNA synthesis and a 5' defined tag sequence for subsequent amplification. Recently, this amplification method was combined with next generation sequencing to obtain viral sequences. However, these studies showed a biased distribution of the resulting sequence reads over the analyzed genomes. The aim of this study was to elucidate the mechanisms that lead to biased sequence depth when using random amplification. Avian paramyxovirus type 8 was used as a model RNA virus to investigate these mechanisms. We showed, based on in silico analysis of the sequence depth in relation to GC-content, predicted RNA secondary structure and sequence complementarity to the 3' part of the tag sequence, that the tag sequence has the main contribution to the observed bias in sequence depth. We confirmed this finding experimentally using both fragmented and non-fragmented viral RNAs as well as primers differing in random oligomer length (6 or 12 nucleotides and in the sequence of the amplification tag. The observed oligonucleotide annealing bias can be reduced by extending the random oligomer sequence and by in silico combining sequence data from SISPA experiments using different 5' defined tag sequences. These findings contribute to the optimization of random nucleic acid amplification protocols that are currently required for downstream applications such as viral metagenomics and microarray analysis.

  20. Aperiodic SiSn/Si multilayers for thermoelectric applications

    Science.gov (United States)

    Tonkikh, A. A.; Zakharov, N. D.; Eisenschmidt, C.; Leipner, H. S.; Werner, P.

    2014-04-01

    We report on novel defect-free SiSn/Si heterostructures grown pseudomorphically on Si(001) substrates using temperature-modulated molecular beam epitaxy. This approach results in a sustainable epitaxial growth for SiSn/Si multilayers. Transmission electron microscopy and electron diffraction manifest that SiSn layers possess a diamond lattice structure. X-ray diffraction reveals up to 9.5 at% Sn in the crystal lattice of SiSn layers.

  1. Influence of Deviation on Optical Transmission through Aperiodic Superlattices

    Institute of Scientific and Technical Information of China (English)

    YIN Hai-Long; YANG Xiang-Bo; LAN Sheng; HU Wei

    2007-01-01

    We propose a deviation model and study the influences of the relative error and sensitivity of a machine on the transmission coefficients (TCs) of Fibonacci superlattices. It is found that for a system with fewer layers, the influence of deviation can be ignored. When superlattices become more complicated, they may be fabricated by a machine with suitable relative error and possess the designed value of TC. However, when the number of system layers exceeds some critical value, superlattices should be manufactured only by precise machines. The influence of the sensitivity is also discussed.

  2. Simulation and quasilinear theory of aperiodic ordinary mode instability

    Energy Technology Data Exchange (ETDEWEB)

    Seough, Jungjoon [Faculty of Human Development, University of Toyama, 3190, Gofuku, Toyama City, Toyama 930-8555 (Japan); International Research Fellow of the Japan Society for the Promotion of Science, Tokyo (Japan); Yoon, Peter H. [Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742 (United States); School of Space Research, Kyung Hee University, Yongin-Si, Gyeonggi-Do 446-701 (Korea, Republic of); Hwang, Junga [Korea Astronomy and Space Science Institute, Daejeon (Korea, Republic of); Department of Astronomy and Space Science, University of Science and Technology, Daejeon (Korea, Republic of); Nariyuki, Yasuhiro [Faculty of Human Development, University of Toyama, 3190, Gofuku, Toyama City, Toyama 930-8555 (Japan)

    2015-08-15

    The purely growing ordinary (O) mode instability driven by excessive parallel temperature anisotropy for high-beta plasmas was first discovered in the 1970s. This instability receives renewed attention because it may be applicable to the solar wind plasma. The electrons in the solar wind feature temperature anisotropies whose upper values are apparently limited by plasma instabilities. The O-mode instability may be important in this regard. Previous studies of O mode instability have been based on linear theory, but the actual solar wind electrons may be in saturated state. The present paper investigates the nonlinear saturation behavior of the O mode instability by means of one-dimensional particle-in-cell simulation and quasilinear theory. It is shown that the quasilinear method accurately reproduces the simulation results.

  3. Quasilinear saturation of the aperiodic ordinary mode streaming instability

    Energy Technology Data Exchange (ETDEWEB)

    Stockem Novo, A., E-mail: anne@tp4.rub.de; Schlickeiser, R. [Institut für Theoretische Physik, Lehrstuhl IV: Weltraum-und Astrophysik, Ruhr-Universität Bochum, D-44780 Bochum (Germany); Yoon, P. H. [Institute for Physical Science & Technology, University of Maryland, College Park, Maryland 20742 (United States); School of Space Research, Kyung Hee University, Yongin-Si, Gyeonggi-Do 446-701 (Korea, Republic of); Lazar, M. [Institut für Theoretische Physik, Lehrstuhl IV: Weltraum-und Astrophysik, Ruhr-Universität Bochum, D-44780 Bochum (Germany); Centre for Mathematical Plasma Astrophysics, Celestijnenlaan 200B, 3001 Leuven (Belgium); Poedts, S. [Centre for Mathematical Plasma Astrophysics, Celestijnenlaan 200B, 3001 Leuven (Belgium); Seough, J. [Faculty of Human Development, University of Toyama, 3190, Gofuku, Toyama City, Toyama 930-8555 (Japan); International Research Fellow of the Japan Society for the Promotion of Science, Tokyo (Japan)

    2015-09-15

    In collisionless plasmas, only kinetic instabilities and fluctuations are effective in reducing the free energy and scatter plasma particles, preventing an increase of their anisotropy. Solar energetic outflows into the interplanetary plasma give rise to important thermal anisotropies and counterstreaming motions of plasma shells, and the resulting instabilities are expected to regulate the expansion of the solar wind. The present paper combines quasilinear theory and kinetic particle-in-cell simulations in order to study the weakly nonlinear saturation of the ordinary mode in hot counter-streaming plasmas with a temperature anisotropy as a follow-up of the paper by Seough et al. [Phys. Plasmas 22, 082122 (2015)]. This instability provides a plausible mechanism for the origin of dominating, two-dimensional spectrum of transverse magnetic fluctuations observed in the solar wind. Stimulated by the differential motion of electron counterstreams the O mode instability may convert their free large-scale energy by nonlinear collisionless dissipation on plasma particles.

  4. Aperiodic Photonic-Plasmonic Structures with Broadband Field Enhancement

    Science.gov (United States)

    2012-10-15

    Fibonacci, (c) Thue-Morse, (d) Rudin - Shapiro arrays at three different normalized wavelengths...standard arrays: periodic, Fibonacci, Thue-Morse, and Rudin -Shapiro with the Wood’s anomaly condition (Equation 5b) plotted for three wavelengths...d) Rudin -Shapiro arrays at three different normalized wavelengths. In Fig 12, the Wood’s anomaly is clearly visible for the periodic array. For

  5. Spontaneous parametric down conversion in chirped, aperiodically-poled crystals

    CERN Document Server

    Sanchez-Lozano, X; U'Ren, Alfred

    2014-01-01

    We present a theoretical analysis of the process of spontaneous parametric down conversion (SPDC) in a non-linear crystal characterized by a linearly-chirped X(2) grating along the direction of propagation. Our analysis leads to an expression for the joint spectral amplitude, based on which we can derive various spectral-temporal properties of the photon pairs and of the heralded single photons obtained from the photon pairs, including: the single photon spectrum, the chronocyclic Wigner function and the Schmidt number. The simulations that we present are for the specific case of a collinear SPDC source based on a PPLN crystal with the signal and idler photons emitted close to the telecom window. We discuss the mechanism for spectral broadening due to the presence of a linearly chirped X(2) grating, showing that not only the width but also to some extent the shape of the SPDC spectrum maybe controlled. Also, we discuss how the fact that the different spectral components are emitted on different planes in the ...

  6. Aperiodic magnetic turbulence produced by relativistic ion beams

    CERN Document Server

    Niemiec, Jacek; Bret, Antoine; Stroman, Thomas

    2009-01-01

    Magnetic-field generation by a relativistic ion beam propagating through an electron-ion plasma along a homogeneous magnetic field is investigated with 2.5D high-resolution particle-in-cell (PIC) simulations. The studies test predictions of a strong amplification of short-wavelength modes of magnetic turbulence upstream of nonrelativistic and relativistic parallel shocks associated with supernova remnants, jets of active galactic nuclei, and gamma-ray bursts. We find good agreement in the properties of the turbulence observed in our simulations compared with the dispersion relation calculated for linear waves with arbitrary orientation of ${\\vec k}$. Depending on the parameters, the backreaction on the ion beam leads to filamentation of the ambient plasma and the beam, which in turn influences the properties of the magnetic turbulence. For mildly- and ultra-relativistic beams, the instability saturates at field amplitudes a few times larger than the homogeneous magnetic field strength. This result matches our...

  7. Properties of Deterministic Aperiodic Photonic Nanostructures for Biosensors

    DEFF Research Database (Denmark)

    Paulsen, Moritz; Jahns, Sabrina; Neustock, Lars Thorben

    for these structures and are compared to the experimental results. [1] Jahns, S., Bräu, M., Meyer, B. O., Karrock, T., Gutekunst, S. B., Blohm, L., Selhuber-Unkel, C., Buhmann, R., Nazirizadeh, Y., Gerken, M. (2015). Handheld imaging photonic crystal biosensor for multiplexed, label-free protein detection. Biomedical...

  8. Aperiodic topological order in the domain configurations of functional materials

    Science.gov (United States)

    Huang, Fei-Ting; Cheong, Sang-Wook

    2017-03-01

    In numerous functional materials, such as steels, ferroelectrics and magnets, new functionalities can be achieved through the engineering of the domain structures, which are associated with the ordering of certain parameters within the material. The recent progress in technologies that enable imaging at atomic-scale spatial resolution has transformed our understanding of domain topology, revealing that, along with simple stripe-like or irregularly shaped domains, intriguing vortex-type topological domain configurations also exist. In this Review, we present a new classification scheme of 'Zm Zn domains with Zl vortices' for 2D macroscopic domain structures with m directional variants and n translational antiphases. This classification, together with the concepts of topological protection and topological charge conservation, can be applied to a wide range of materials, such as multiferroics, improper ferroelectrics, layered transition metal dichalcogenides and magnetic superconductors, as we discuss using selected examples. The resulting topological considerations provide a new basis for the understanding of the formation, kinetics, manipulation and property optimization of domains and domain boundaries in functional materials.

  9. Sequences in language and text

    CERN Document Server

    Mikros, George K

    2015-01-01

    The aim of this volume is to present the diverse but highly interesting area of the quantitative analysis of the sequence of various linguistic structures. The collected articles present a wide spectrum of quantitative analyses of linguistic syntagmatic structures and explore novel sequential linguistic entities. This volume will be interesting to all researchers studying linguistics using quantitative methods.

  10. Instruction Sequences for Computer Science

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2012-01-01

    This book demonstrates that the concept of an instruction sequence offers a novel and useful viewpoint on issues relating to diverse subjects in computer science. Selected issues relating to well-known subjects from the theory of computation and the area of computer architecture are rigorously

  11. Single-primer fluorescent sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Ruth, J.L.; Morgan, C.A.; Middendorf, L.R.; Grone, D.L.; Brumbaugh, J.A.

    1987-05-01

    Modified linker arm oligonucleotides complementary to standard M13 priming sites were synthesized, labelled with either one, two, or three fluoresceins, and purified by reverse-phase HPLC. When used as primers in standard dideoxy M13 sequencing with /sup 32/P-dNTPs, normal autoradiographic patterns were obtained. To eliminate the radioactivity, direct on-line fluorescence detection was achieved by the use of a scanning 10 mW Argon laser emitting 488 nm light. Fluorescent bands were detected directly in standard 0.2 or 0.35 mm thick polyacrylamide gels at a distance of 24 cm from the loading wells by a photomultiplier tube filtered at 520 nm. Horizontal and temporal location of each band was displayed by computer as a band in real time, providing visual appearance similar to normal 4-lane autoradiograms. Using a single primer labelled with two fluoresceins, sequences of between 500 and 600 bases have been read in a single loading with better than 98% accuracy; up to 400 bases can be read reproducibly with no errors. More than 50 sequences have been determined by this method. This approach requires only 1-2 ug of cloned template, and produces continuous sequence data at about one band per minute.

  12. Multifractal analyses of music sequences

    Science.gov (United States)

    Su, Zhi-Yuan; Wu, Tzuyin

    2006-09-01

    Multifractal analysis is applied to study the fractal property of music. In this paper, a method is proposed to transform both the melody and rhythm of a music piece into individual sets of distributed points along a one-dimensional line. The structure of the musical composition is thus manifested and characterized by the local clustering pattern of these sequences of points. Specifically, the local Hölder exponent and the multifractal spectrum are calculated for the transformed music sequences according to the multifractal formalism. The observed fluctuations of the Hölder exponent along the music sequences confirm the non-uniformity feature in the structures of melodic and rhythmic motions of music. Our present result suggests that the shape and opening width of the multifractal spectrum plot can be used to distinguish different styles of music. In addition, a characteristic curve is constructed by mapping the point sequences converted from the melody and rhythm of a musical work into a two-dimensional graph. Each different pieces of music has its own unique characteristic curve. This characteristic curve, which also exhibits a fractal trait, unveils the intrinsic structure of music.

  13. Fractals in DNA sequence analysis

    Institute of Scientific and Technical Information of China (English)

    Yu Zu-Guo(喻祖国); Vo Anh; Gong Zhi-Min(龚志民); Long Shun-Chao(龙顺潮)

    2002-01-01

    Fractal methods have been successfully used to study many problems in physics, mathematics, engineering, finance,and even in biology. There has been an increasing interest in unravelling the mysteries of DNA; for example, how can we distinguish coding and noncoding sequences, and the problems of classification and evolution relationship of organisms are key problems in bioinformatics. Although much research has been carried out by taking into consideration the long-range correlations in DNA sequences, and the global fractal dimension has been used in these works by other people, the models and methods are somewhat rough and the results are not satisfactory. In recent years, our group has introduced a time series model (statistical point of view) and a visual representation (geometrical point of view)to DNA sequence analysis. We have also used fractal dimension, correlation dimension, the Hurst exponent and the dimension spectrum (multifractal analysis) to discuss problems in this field. In this paper, we introduce these fractal models and methods and the results of DNA sequence analysis.

  14. Farey Sequences and Resistor Networks

    Indian Academy of Sciences (India)

    Sameen Ahmed Khan

    2012-05-01

    In this article, we employ the Farey sequence and Fibonacci numbers to establish strict upper and lower bounds for the order of the set of equivalent resistances for a circuit constructed from equal resistors combined in series and in parallel. The method is applicable for networks involving bridge and non-planar circuits.

  15. The Toothpick Sequence and Other Sequences from Cellular Automata

    CERN Document Server

    Applegate, David; Sloane, N J A

    2010-01-01

    A two-dimensional arrangement of toothpicks is constructed by the following iterative procedure. At stage 1, place a single toothpick of length 1 on a square grid, aligned with the y-axis. At each subsequent stage, for every exposed toothpick end, place an orthogonal toothpick centered at that end. The resulting structure has a fractal-like appearance. We will analyze the toothpick sequence, which gives the total number of toothpicks after n steps. We also study several related sequences that arise from enumerating active cells in cellular automata. Some unusual recurrences appear: a typical example is that instead of the Fibonacci recurrence, which we may write as a(2+i) = a(i) + a(i+1), we set n = 2^k+i (0 = 0} (1+x^{2^k-1}+2x^{2^k}) and variations thereof.

  16. Algebraic divisibility sequences over function fields

    CERN Document Server

    Ingram, Patrick; Silverman, Joseph H; Stange, Katherine E; Streng, Marco

    2011-01-01

    We study the existence of primes and of primitive divisors in classical divisibility sequences defined over function fields. Under various hypotheses, we prove that Lucas sequences and elliptic divisibility sequences over function fields defined over number fields contain infinitely many irreducible elements. We also prove that an elliptic divisibility sequence over a function field has only finitely many terms lacking a primitive divisor.

  17. Stream cipher based on GSS sequences

    Institute of Scientific and Technical Information of China (English)

    HU Yupu; XIAO Guozhen

    2004-01-01

    Generalized self-shrinking sequences, simply named the GSS sequences,are novel periodic sequences that have many advantages in cryptography. In this paper,we give several results about GSS sequence's application to cryptography. First, we give a simple method for selecting those GSS sequences whose least periods reach the maximum. Second, we give a method for describing and computing the auto-correlation coefficients of GSS sequences. Finally, we point out that some GSS sequences, when used as stream ciphers, have a security weakness.

  18. Pig genome sequence - analysis and publication strategy

    DEFF Research Database (Denmark)

    Archibald, Alan L.; Bolund, Lars; Churcher, Carol;

    2010-01-01

    BACKGROUND: The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing. RESULTS: Assemblies......) is under construction and will incorporate whole genome shotgun sequence (WGS) data providing > 30x genome coverage. The WGS sequence, most of which comprise short Illumina/Solexa reads, were generated from DNA from the same single Duroc sow as the source of the BAC library from which clones were...

  19. Sequence-structure relations of biopolymers

    CERN Document Server

    Barrett, Christopher; Reidys, Christian M

    2015-01-01

    Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as structural semantics of sequence data that allows for a different interpretation than conventional sequence alignment. Structural semantics could enable us to identify more general embedded "patterns" in DNA and RNA sequences. Results: We compute the partition function of sequences with respect to a fixed structure and connect this computation to the mutual information of a sequence-structure pair for RNA secondary structures. We present a Boltzmann sampler and obtain the a priori probability of specific sequence patterns. We present a detailed analysis for the three PDB-structures, 2JXV (hairpin), 2N3R (3-branch multi-loop) and 1EHZ (tRNA). We localize specific sequence patterns, contrast the energy spectrum of the Boltzmann sampled sequences versus those sequences that refold ...

  20. Expressing stochastic filters via number sequences

    OpenAIRE

    Capponi, A.; Farina, A; Pilotto, C.

    2010-01-01

    We generalize the results presented in [1] regarding the relation between the Kalman filter and the Fibonacci sequence. We consider more general filtering models and relate the finite dimensional Kalman and Benes filters to the Fibonacci sequence and to the Golden Section. We also prove that Fibonacci numbers may be expressed as the convolution of the Fibonacci and Padovan sequence, thus extending the connection between stochastic filtering and Fibonacci sequence to the Padovan sequence.

  1. Cassini Mission Sequence Subsystem (MSS)

    Science.gov (United States)

    Alland, Robert

    2011-01-01

    This paper describes my work with the Cassini Mission Sequence Subsystem (MSS) team during the summer of 2011. It gives some background on the motivation for this project and describes the expected benefit to the Cassini program. It then introduces the two tasks that I worked on - an automatic system auditing tool and a series of corrections to the Cassini Sequence Generator (SEQ_GEN) - and the specific objectives these tasks were to accomplish. Next, it details the approach I took to meet these objectives and the results of this approach, followed by a discussion of how the outcome of the project compares with my initial expectations. The paper concludes with a summary of my experience working on this project, lists what the next steps are, and acknowledges the help of my Cassini colleagues.

  2. Nonparametric Inference for Periodic Sequences

    KAUST Repository

    Sun, Ying

    2012-02-01

    This article proposes a nonparametric method for estimating the period and values of a periodic sequence when the data are evenly spaced in time. The period is estimated by a "leave-out-one-cycle" version of cross-validation (CV) and complements the periodogram, a widely used tool for period estimation. The CV method is computationally simple and implicitly penalizes multiples of the smallest period, leading to a "virtually" consistent estimator of integer periods. This estimator is investigated both theoretically and by simulation.We also propose a nonparametric test of the null hypothesis that the data have constantmean against the alternative that the sequence of means is periodic. Finally, our methodology is demonstrated on three well-known time series: the sunspots and lynx trapping data, and the El Niño series of sea surface temperatures. © 2012 American Statistical Association and the American Society for Quality.

  3. Genome Sequence of Mycobacteriophage Momo.

    Science.gov (United States)

    Pope, Welkin H; Bina, Elizabeth A; Brahme, Indraneel S; Hill, Amy B; Himmelstein, Philip H; Hunsicker, Sara M; Ish, Amanda R; Le, Tinh S; Martin, Mary M; Moscinski, Catherine N; Shetty, Sameer A; Swierzewski, Tomasz; Iyengar, Varun B; Kim, Hannah; Schafer, Claire E; Grubb, Sarah R; Warner, Marcie H; Bowman, Charles A; Russell, Daniel A; Hatfull, Graham F

    2015-06-18

    Momo is a newly discovered phage of Mycobacterium smegmatis mc(2)155. Momo has a double-stranded DNA genome 154,553 bp in length, with 233 predicted protein-encoding genes, 34 tRNA genes, and one transfer-messenger RNA (tmRNA) gene. Momo has a myoviral morphology and shares extensive nucleotide sequence similarity with subcluster C1 mycobacteriophages. Copyright © 2015 Pope et al.

  4. Multiplicative LSTM for sequence modelling

    OpenAIRE

    Krause, Ben; Lu, Liang; Murray, Iain; Renals, Steve

    2016-01-01

    This paper introduces multiplicative LSTM, a novel hybrid recurrent neural network architecture for sequence modelling that combines the long short-term memory (LSTM) and multiplicative recurrent neural network architectures. Multiplicative LSTM is motivated by its flexibility to have very different recurrent transition functions for each possible input, which we argue helps make it more expressive in autoregressive density estimation. We show empirically that multiplicative LSTM outperforms ...

  5. Multineuronal Spike Sequences Repeat with Millisecond Precision

    Directory of Open Access Journals (Sweden)

    Koki eMatsumoto

    2013-06-01

    Full Text Available Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and nonspiking neurons. Multineuronal spike sequences were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.

  6. Method and apparatus for biological sequence comparison

    Science.gov (United States)

    Marr, T.G.; Chang, W.I.

    1997-12-23

    A method and apparatus are disclosed for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence. 5 figs.

  7. Static multiplicities in heterogeneous azeotropic distillation sequences

    DEFF Research Database (Denmark)

    Esbjerg, Klavs; Andersen, Torben Ravn; Jørgensen, Sten Bay

    1998-01-01

    In this paper the results of a bifurcation analysis on heterogeneous azeotropic distillation sequences are given. Two sequences suitable for ethanol dehydration are compared: The 'direct' and the 'indirect' sequence. It is shown, that the two sequences, despite their similarities, exhibit very...... different static behavior. The method of Petlyuk and Avet'yan (1971), Bekiaris et al. (1993), which assumes infinite reflux and infinite number of stages, is extended to and applied on heterogeneous azeotropic distillation sequences. The predictions are substantiated through simulations. The static sequence...

  8. On Inclusion Relations between Some Sequence Spaces

    Directory of Open Access Journals (Sweden)

    R. Çolak

    2016-01-01

    Full Text Available We determine the relations between the classes S^λ of almost λ-statistically convergent sequences and the relations between the classes V^,λ of strongly almost V,λ-summable sequences for various sequences λ, μ in the class Λ. Furthermore we also give the relations between the classes S^λ of almost λ-statistically convergent sequences and the classes V^,λ of strongly almost V,λ-summable sequences for various sequences λ,μ∈Λ.

  9. Bernoulli measure of complex admissible kneading sequences

    CERN Document Server

    Bruin, Henk

    2012-01-01

    Iterated quadratic polynomials give rise to a rich collection of different dynamical systems that are parametrized by a simple complex parameter $c$. The different dynamical features are encoded by the \\emph{kneading sequence} which is an infinite sequence over $\\{0,\\1\\}$. Not every such sequence actually occurs in complex dynamics. The set of admissible kneading sequences was described by Milnor and Thurston for real quadratic polynomials, and by the authors in the complex case. We prove that the set of admissible kneading sequences has positive Bernoulli measure within the set of sequences over $\\{0,\\1\\}$.

  10. Blind sequence-length estimation of low-SNR cyclostationary sequences

    CSIR Research Space (South Africa)

    Vlok, JD

    2014-06-01

    Full Text Available Several existing direct-sequence spread spectrum (DSSS) detection and estimation algorithms assume prior knowledge of the symbol period or sequence length, although very few sequence-length estimation techniques are available in the literature...

  11. Modified Genetic Algorithm for DNA Sequence Assembly by Shotgun and Hybridization Sequencing Techniques

    Directory of Open Access Journals (Sweden)

    Prof.Narayan Kumar Sahu

    2012-09-01

    Full Text Available Since the advent of rapid DNA sequencing methods in 1976, scientists have had the problem of inferring DNA sequences from sequenced fragments. Shotgun sequencing is a well-established biological and computational method used in practice. Many conventional algorithms for shotgun sequencing are based on the notion of pair wise fragment overlap. While shotgun sequencing infers a DNA sequence given the sequences of overlapping fragments, a recent and complementary method, called sequencing by hybridization (SBH, infers a DNA sequence given the set of oligomers that represents all sub words of some fixed length, k. In this paper, we propose a new computer algorithm for DNA sequence assembly that combines in a novel way the techniques of both shotgun and SBH methods. Based on our preliminary investigations, the algorithm promises- to be very fast and practical for DNA sequence assembly [1].

  12. Biomolecule Sequencer: Nanopore Sequencing Technology for In-Situ Environmental Monitoring and Astrobiology

    Science.gov (United States)

    John, K. K.; Botkin, D. J.; Burton, A. S.; Castro-Wallace, S. L.; Chaput, J. D.; Dworkin, J. P.; Lupisella, M. L.; Mason, C. E.; Rubins, K. H.; Smith, D. J.; Stahl, S.; Switzer, C.

    2016-10-01

    Biomolecule Sequencer will demonstrate, for the first time, that DNA sequencing is feasible as a tool for in-situ environmental monitoring and astrobiology. A space-based sequencer could identify microbes, diseases, and help detect DNA-based life.

  13. Integration of retinal image sequences

    Science.gov (United States)

    Ballerini, Lucia

    1998-10-01

    In this paper a method for noise reduction in ocular fundus image sequences is described. The eye is the only part of the human body where the capillary network can be observed along with the arterial and venous circulation using a non invasive technique. The study of the retinal vessels is very important both for the study of the local pathology (retinal disease) and for the large amount of information it offers on systematic haemodynamics, such as hypertension, arteriosclerosis, and diabetes. In this paper a method for image integration of ocular fundus image sequences is described. The procedure can be divided in two step: registration and fusion. First we describe an automatic alignment algorithm for registration of ocular fundus images. In order to enhance vessel structures, we used a spatially oriented bank of filters designed to match the properties of the objects of interest. To evaluate interframe misalignment we adopted a fast cross-correlation algorithm. The performances of the alignment method have been estimated by simulating shifts between image pairs and by using a cross-validation approach. Then we propose a temporal integration technique of image sequences so as to compute enhanced pictures of the overall capillary network. Image registration is combined with image enhancement by fusing subsequent frames of a same region. To evaluate the attainable results, the signal-to-noise ratio was estimated before and after integration. Experimental results on synthetic images of vessel-like structures with different kind of Gaussian additive noise as well as on real fundus images are reported.

  14. Discrete low-discrepancy sequences

    CERN Document Server

    Angel, Omer; Martin, James B; Propp, James

    2009-01-01

    Holroyd and Propp used Hall's marriage theorem to show that, given a probability distribution pi on a finite set S, there exists an infinite sequence s_1,s_2,... in S such that for all integers k >= 1 and all s in S, the number of i in [1,k] with s_i = s differs from k pi(s) by at most 1. We prove a generalization of this result using a simple explicit algorithm. A special case of this algorithm yields an extension of Holroyd and Propp's result to the case of discrete probability distributions on infinite sets.

  15. Infinite matrices and sequence spaces

    CERN Document Server

    Cooke, Richard G

    2014-01-01

    This clear and correct summation of basic results from a specialized field focuses on the behavior of infinite matrices in general, rather than on properties of special matrices. Three introductory chapters guide students to the manipulation of infinite matrices, covering definitions and preliminary ideas, reciprocals of infinite matrices, and linear equations involving infinite matrices.From the fourth chapter onward, the author treats the application of infinite matrices to the summability of divergent sequences and series from various points of view. Topics include consistency, mutual consi

  16. Differential correlation for sequencing data.

    Science.gov (United States)

    Siska, Charlotte; Kechris, Katerina

    2017-01-19

    Several methods have been developed to identify differential correlation (DC) between pairs of molecular features from -omics studies. Most DC methods have only been tested with microarrays and other platforms producing continuous and Gaussian-like data. Sequencing data is in the form of counts, often modeled with a negative binomial distribution making it difficult to apply standard correlation metrics. We have developed an R package for identifying DC called Discordant which uses mixture models for correlations between features and the Expectation Maximization (EM) algorithm for fitting parameters of the mixture model. Several correlation metrics for sequencing data are provided and tested using simulations. Other extensions in the Discordant package include additional modeling for different types of differential correlation, and faster implementation, using a subsampling routine to reduce run-time and address the assumption of independence between molecular feature pairs. With simulations and breast cancer miRNA-Seq and RNA-Seq data, we find that Spearman's correlation has the best performance among the tested correlation methods for identifying differential correlation. Application of Spearman's correlation in the Discordant method demonstrated the most power in ROC curves and sensitivity/specificity plots, and improved ability to identify experimentally validated breast cancer miRNA. We also considered including additional types of differential correlation, which showed a slight reduction in power due to the additional parameters that need to be estimated, but more versatility in applications. Finally, subsampling within the EM algorithm considerably decreased run-time with negligible effect on performance. A new method and R package called Discordant is presented for identifying differential correlation with sequencing data. Based on comparisons with different correlation metrics, this study suggests Spearman's correlation is appropriate for sequencing data

  17. Asymptotics of Lagged Fibonacci Sequences

    CERN Document Server

    Mertens, Stephan

    2009-01-01

    Consider "lagged" Fibonacci sequences $a(n) = a(n-1)+a(\\lfloor n/k\\rfloor)$ for $k > 1$. We show that $\\lim_{n\\to\\infty} a(kn)/a(n)\\cdot\\ln n/n = k\\ln k$ and we demonstrate the slow numerical convergence to this limit and how to deal with this slow convergence. We also discuss the connection between two classical results of N.G. de Bruijn and K. Mahler on the asymptotics of $a(n)$.

  18. FOGSAA: Fast Optimal Global Sequence Alignment Algorithm

    Science.gov (United States)

    Chakraborty, Angana; Bandyopadhyay, Sanghamitra

    2013-04-01

    In this article we propose a Fast Optimal Global Sequence Alignment Algorithm, FOGSAA, which aligns a pair of nucleotide/protein sequences faster than any optimal global alignment method including the widely used Needleman-Wunsch (NW) algorithm. FOGSAA is applicable for all types of sequences, with any scoring scheme, and with or without affine gap penalty. Compared to NW, FOGSAA achieves a time gain of (70-90)% for highly similar nucleotide sequences (> 80% similarity), and (54-70)% for sequences having (30-80)% similarity. For other sequences, it terminates with an approximate score. For protein sequences, the average time gain is between (25-40)%. Compared to three heuristic global alignment methods, the quality of alignment is improved by about 23%-53%. FOGSAA is, in general, suitable for aligning any two sequences defined over a finite alphabet set, where the quality of the global alignment is of supreme importance.

  19. Genome Sequences of Eight Morphologically Diverse Alphaproteobacteria▿

    OpenAIRE

    Brown, Pamela J.B.; Kysela, David T.; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V

    2011-01-01

    The Alphaproteobacteriacomprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium.

  20. Genome sequences of eight morphologically diverse Alphaproteobacteria.

    Science.gov (United States)

    Brown, Pamela J B; Kysela, David T; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V

    2011-09-01

    The Alphaproteobacteria comprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium.

  1. Genome Sequences of Eight Morphologically Diverse Alphaproteobacteria▿

    Science.gov (United States)

    Brown, Pamela J. B.; Kysela, David T.; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V.

    2011-01-01

    The Alphaproteobacteriacomprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium. PMID:21705585

  2. The Art of Gymnastics: Creating Sequences.

    Science.gov (United States)

    Rovegno, Inez

    1988-01-01

    Offering students opportunities for creating movement sequences in gymnastics allows them to understand the essence of gymnastics, have creative experiences, and learn about themselves. The process of creating sequences is described. (MT)

  3. CONSONANT SEQUENCE REDUCTION IN CHILD PHONOLOGY

    African Journals Online (AJOL)

    Dr Kola ADENIYI

    in children's developmental difficulties, it is apparent that their vocal tracts are not ... proper articulation of certain complex sounds or sound sequences. ...... the nasal-oral consonant sequence is even limited in Yoruba, it means the frequency of.

  4. On topological spaces possessing uniformly distributed sequences

    CERN Document Server

    Bogachev, V I

    2007-01-01

    Two classes of topological spaces are introduced on which every probability Radon measure possesses a uniformly distributed sequence or a uniformly tight uniformly distributed sequence. It is shown that these classes are stable under multiplication by completely regular Souslin spaces

  5. On General Fibonacci Sequences in Groups

    OpenAIRE

    Özkan, Engin

    2003-01-01

    In this paper, we have constituted 3-step general Fibonacci sequences in a nilpotent group with exponent p (p is a prime number) and nilpotency class 4 and given formulas to find the a term of the sequence.

  6. On Paranorm Zweier -Convergent Sequence Spaces

    Directory of Open Access Journals (Sweden)

    Vakeel A. Khan

    2013-01-01

    Full Text Available In this paper, we introduce the paranorm Zweier -convergent sequence spaces , , and , a sequence of positive real numbers. We study some topological properties, prove the decomposition theorem, and study some inclusion relations on these spaces.

  7. Strong sequences and independent sets

    Directory of Open Access Journals (Sweden)

    Joanna Jureczko

    2016-05-01

    Full Text Available A family $\\mathcal{S} \\in \\mathcal{P}(\\omega$ is \\textit{an independent family} if for each pair $\\mathcal{A, B}$ of disjoint finite subsets of $\\mathcal{S}$ the set $\\bigcap \\mathcal{A} \\cap (\\omega \\setminus \\bigcup \\mathcal{B}$ is nonempty. The fact that there is an independent family on $\\omega$ of size continuum was proved by Fichtenholz and Kantorowicz in \\cite{FK}. If we substitute $\\mathcal{P}(\\omega$ by a set $(X, r$ with arbitrary relation \\textit{r} it is natural question about existence and length of an independent set on $(X, r$. In this paper special assumptions of such existence will be considered. On the other hand in 60s' of the last century the strong sequences method was introduced by Efimov. He used it for proving some famous theorems in dyadic spaces like: Marczewski theorem on cellularity, Shanin theorem on a calibre, Esenin-Volpin theorem and others. In this paper there will be considered: length of strong sequences, the length of independent sets and other well known cardinal invariants and there will be examined inequalities among them.

  8. Sequence Analysis in Demographic Research

    Directory of Open Access Journals (Sweden)

    Billari, Francesco C.

    2001-01-01

    Full Text Available EnglishThis paper examines the salient features of sequence analysis in demogrpahicresearch. The new approach allows a holistic perspective on life course analysis and is based on arepresentation of lives as sequences of states. Some of the methods for analyzing such data aresketched, from complex description to optimal matching ot monoethetic divisive algorithms. Afer ashort ilustration of a demographically-relevant example, the needs in terms of data collection and theopportunities of applying the same aproach to synthetic data are discussed.FrenchOn examine ici les principaux éléments de l’analyse par séquence endémographie. Cette nouvelle technique permet une perspective unifiée del’analyse du cours de la vie, en représentant la vie comme une série d’états.Certaines des méthodes pour de telles analyses sont décrites, en commençant parla description complexe, pour considérer ensuite les alignements optimales, etles algorithmes de division. Après un court exemple en démographie, onconsidère les besoins en données et les possibilités d’application aux donnéessynthétique.

  9. Information Analysis of DNA Sequences

    CERN Document Server

    Mohammed, Riyazuddin

    2010-01-01

    The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they do not seem to participate in the process of transcription of amino-acids, they have been termed "junk DNA." Although it is believed that the non-coding regions in genomes have no role in cell growth and evolution, demonstration that these regions carry useful information would tend to falsify this belief. In this paper, we consider entropy as a measure of information by modifying the entropy expression to take into account the varying length of these sequences. Exons are usually much shorter in length than introns; therefore the comparison of the entropy values needs to be normalized. A length correction strategy was employed using randomly generated nucleonic base strings built out of the alphabet of the same size as the exons under question. Our analysis shows that intron...

  10. Movement sequencing in Huntington disease.

    Science.gov (United States)

    Georgiou-Karistianis, Nellie; Long, Jeffrey D; Lourens, Spencer G; Stout, Julie C; Mills, James A; Paulsen, Jane S

    2014-08-01

    To examine longitudinal changes in movement sequencing in prodromal Huntington's disease (HD) participants (795 prodromal HD; 225 controls) from the PREDICT-HD study. Prodromal HD participants were tested over seven annual visits and were stratified into three groups (low, medium, high) based on their CAG-Age Product (CAP) score, which indicates likely increasing proximity to diagnosis. A cued movement sequence task assessed the impact of advance cueing on response initiation and execution via three levels of advance information. Compared to controls, all CAP groups showed longer initiation and movement times across all conditions at baseline, demonstrating a disease gradient for the majority of outcomes. Across all conditions, the high CAP group had the highest mean for baseline testing, but also demonstrated an increase in movement time across the study. For initiation time, the high CAP group showed the highest mean baseline time across all conditions, but also faster decreasing rates of change over time. With progress to diagnosis, participants may increasingly use compensatory strategies, as evidenced by faster initiation. However, this occurred in conjunction with slowed execution times, suggesting a decline in effectively accessing control processes required to translate movement into effective execution.

  11. Effects of Sequence Partitioning on Compression Rate

    CERN Document Server

    Alagoz, B Baykant

    2010-01-01

    In the paper, a theoretical work is done for investigating effects of splitting data sequence into packs of data set. We proved that a partitioning of data sequence is possible to find such that the entropy rate at each subsequence is lower than entropy rate of the source. Effects of sequence partitioning on overall compression rate are argued on the bases of partitioning statistics, and then, an optimization problem for an optimal partition is defined to improve overall compression rate of a sequence.

  12. Cross-correlation properties of cyclotomic sequences

    CERN Document Server

    Cai, Kai; Zheng, Zhiming

    2009-01-01

    Sequences with good correlation properties are widely used in engineering applications, especially in the area of communications. Among the known sequences, cyclotomic families have the optimal autocorrelation property. In this paper, we decide the cross-correlation function of the known cyclotomic sequences completely. Moreover, to get our results, the relations between the multiplier group and the decimations of the characteristic sequence are also established for an arbitrary difference set.

  13. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

    Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.;

    2008-01-01

    Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment me...

  14. Incidental Sequence Learning across the Lifespan

    Science.gov (United States)

    Weiermann, Brigitte; Meier, Beat

    2012-01-01

    The purpose of the present study was to investigate incidental sequence learning across the lifespan. We tested 50 children (aged 7-16), 50 young adults (aged 20-30), and 50 older adults (aged >65) with a sequence learning paradigm that involved both a task and a response sequence. After several blocks of practice, all age groups slowed down…

  15. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    NARCIS (Netherlands)

    Hasan, L.

    2011-01-01

    Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of pr

  16. Disease gene identification strategies for exome sequencing

    NARCIS (Netherlands)

    Gilissen, C.; Hoischen, A.; Brunner, H.G.; Veltman, J.A.

    2012-01-01

    Next generation sequencing can be used to search for Mendelian disease genes in an unbiased manner by sequencing the entire protein-coding sequence, known as the exome, or even the entire human genome. Identifying the pathogenic mutation amongst thousands to millions of genomic variants is a major c

  17. PacBio Sequencing and Its Applications

    Institute of Scientific and Technical Information of China (English)

    Anthony Rhoads; Kin Fai Au

    2015-01-01

    Single-molecule, real-time sequencing developed by Pacific BioSciences offers longer read lengths than the second-generation sequencing (SGS) technologies, making it well-suited for unsolved problems in genome, transcriptome, and epigenetics research. The highly-contiguous de novo assemblies using PacBio sequencing can close gaps in current reference assemblies and characterize structural variation (SV) in personal genomes. With longer reads, we can sequence through extended repetitive regions and detect mutations, many of which are associated with dis-eases. Moreover, PacBio transcriptome sequencing is advantageous for the identification of gene isoforms and facilitates reliable discoveries of novel genes and novel isoforms of annotated genes, due to its ability to sequence full-length transcripts or fragments with significant lengths. Addition-ally, PacBio’s sequencing technique provides information that is useful for the direct detection of base modifications, such as methylation. In addition to using PacBio sequencing alone, many hybrid sequencing strategies have been developed to make use of more accurate short reads in conjunction with PacBio long reads. In general, hybrid sequencing strategies are more affordable and scalable especially for small-size laboratories than using PacBio Sequencing alone. The advent of PacBio sequencing has made available much information that could not be obtained via SGS alone.

  18. Joint Sequence Analysis: Association and Clustering

    Science.gov (United States)

    Piccarreta, Raffaella

    2017-01-01

    In its standard formulation, sequence analysis aims at finding typical patterns in a set of life courses represented as sequences. Recently, some proposals have been introduced to jointly analyze sequences defined on different domains (e.g., work career, partnership, and parental histories). We introduce measures to evaluate whether a set of…

  19. RNAome sequencing delineates the complete RNA landscape

    NARCIS (Netherlands)

    K.W.J. Derks (Kasper); J. Pothof (Joris)

    2015-01-01

    textabstractStandard RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species. For example, small and large RNAs from the same sample cannot be sequenced in a single sequence run. We designed RNAome sequencing, which is a strand-specif

  20. The recurrence sequence via the Fibonacci groups

    Science.gov (United States)

    Aküzüm, Yeşim; Deveci, Ömür

    2016-04-01

    This work develops properties of the recurrence sequence defined by the aid of the relation matrix of the Fibonacci groups. The study of this sequence modulo m yields cyclic groups and semigroups from generating matrix. Finally, we extend the sequence defined to groups and then, we obtain its period in the Fibonacci groups.

  1. Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

    Directory of Open Access Journals (Sweden)

    Leho Tedersoo

    Full Text Available Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/ for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/, the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

  2. Exome sequencing: what clinicians need to know

    Directory of Open Access Journals (Sweden)

    Sastre L

    2014-03-01

    Full Text Available Leandro SastreInstituto de Investigaciones Biomédicas, CSIC/UAM, C/Arturo Duperier 4, Madrid, Spain; Terapias Experimentales y Biomarcadores en Cáncer, IdiPaz, Madrid, Spain; CIBER de Enfermedades Raras, CIBERER, Valencia, SpainAbstract: The recent development of high throughput methods of deoxyribonucleic acid (DNA sequencing has made it possible to determine individual genome sequences and their specific variations. A region of particular interest is the protein-coding part of the genome, or exome, which is composed of gene exons. The principles of exome purification and sequencing will be described in this review, as well as analyses of the data generated. Results will be discussed in terms of their possible functional and clinical significance. The advantages and limitations of exome sequencing will be compared to those of other massive sequencing approaches such as whole-genome sequencing, ribonucleic acid sequencing or selected DNA sequencing. Exome sequencing has been used recently in the study of various diseases. Monogenic diseases with Mendelian inheritance are among these, but studies have also been carried out on genetic variations that represent risk factors for complex diseases. Cancer is another intensive area for exome sequencing studies. Several examples of the use of exome sequencing in the diagnosis, prognosis, and treatment of these diseases will be described. Finally, remaining challenges and some practical and ethical considerations for the clinical application of exome sequencing will be discussed.Keywords: massively parallel sequencing, RNA sequencing, whole-genome sequencing, genetic variants, molecular diagnosis, pharmacogenomics, personalized medicine, NGS, SGS, SNP, SNV

  3. Chip-based sequencing nucleic acids

    Energy Technology Data Exchange (ETDEWEB)

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  4. MatrixPlot: visualizing sequence constraints

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole

    1999-01-01

    MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...... about the sequences (e.g. a sequence logo profile) along the edges of the plot, as well as zoom in on any region in the plot. Availability : MatrixPlot can be obtained on request, and can also be accessed online at http://www. cbs.dtu.dk/services/MatrixPlot. Contact : gorodkin@cbs.dtu.dk...

  5. Chip-based sequencing nucleic acids

    Science.gov (United States)

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  6. MatrixPlot: visualizing sequence constraints

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole

    1999-01-01

    MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...... about the sequences (e.g. a sequence logo profile) along the edges of the plot, as well as zoom in on any region in the plot. Availability : MatrixPlot can be obtained on request, and can also be accessed online at http://www. cbs.dtu.dk/services/MatrixPlot. Contact : gorodkin@cbs.dtu.dk...

  7. Permutation Entropy for Random Binary Sequences

    Directory of Open Access Journals (Sweden)

    Lingfeng Liu

    2015-12-01

    Full Text Available In this paper, we generalize the permutation entropy (PE measure to binary sequences, which is based on Shannon’s entropy, and theoretically analyze this measure for random binary sequences. We deduce the theoretical value of PE for random binary sequences, which can be used to measure the randomness of binary sequences. We also reveal the relationship between this PE measure with other randomness measures, such as Shannon’s entropy and Lempel–Ziv complexity. The results show that PE is consistent with these two measures. Furthermore, we use PE as one of the randomness measures to evaluate the randomness of chaotic binary sequences.

  8. Computing with Hereditarily Finite Sequences

    CERN Document Server

    Tarau, Paul

    2011-01-01

    e use Prolog as a flexible meta-language to provide executable specifications of some fundamental mathematical objects and their transformations. In the process, isomorphisms are unraveled between natural numbers and combinatorial objects (rooted ordered trees representing hereditarily finite sequences and rooted ordered binary trees representing G\\"odel's System {\\bf T} types). This paper focuses on an application that can be seen as an unexpected "paradigm shift": we provide recursive definitions showing that the resulting representations are directly usable to perform symbolically arbitrary-length integer computations. Besides the theoretically interesting fact of "breaking the arithmetic/symbolic barrier", the arithmetic operations performed with symbolic objects like trees or types turn out to be genuinely efficient -- we derive implementations with asymptotic performance comparable to ordinary bitstring implementations of arbitrary-length integer arithmetic. The source code of the paper, organized as a ...

  9. [DNA sequencing technology and automatization of it].

    Science.gov (United States)

    Kraev, A S

    1991-01-01

    Precise manipulations with genetic material, typical for modern experiments in molecular biology and in new biotechnology, require a capability to determine DNA base sequence. This capability enables today to exploit specific genetic knowledge for the dissection of complex cell processes and for modulation of cell metabolism in transgenic organisms. The review focuses on such DNA sequencing technologies that are widespread in general laboratory practice. They can safely be called, with the availability of commercial reagents, industrial techniques. Modern DNA sequencing requires recurrent breakdown of large genomic DNA into smaller pieces, that are then amplified, sequenced and the initial long stretch reconstructed via overlap of small pieces. The DNA sequencing process has several steps: a DNA fragment is obtained in sufficient quantity and purity, it is converted to a form suitable for a particular sequencing method, a sequencing reaction is performed and its products fractionated; and finally the resultant data are interpreted (i.e. an autoradiograph is read into a computer memory) and a long sequence in reconstructed via overlap of short stretches. These steps are considered in separate parts; an accent is made on sequencing strategies with respect to their biological task. In the last part, possibilities for automation of sequencing experiment are considered, followed by a discussion of domestic problems in DNA sequencing.

  10. Experimental investigation of an RNA sequence space

    Science.gov (United States)

    Lee, Youn-Hyung; Dsouza, Lisa; Fox, George E.

    1993-12-01

    Modern rRNAs are the historic consequence of an ongoing evolutionary exploration of a sequence space. These extant sequences belong to a special subset of the sequence space that is comprised only of those primary sequences that can validly perform the biological function(s) required of the particular RNA. If it were possible to readily identify all such valid sequences, stochastic predictions could be made about the relative likelihood of various evolutionary pathways available to an RNA. Herein an experimental system which can assess whether a particular sequence is likely to have validity as a eubacterial 5S rRNA is described. A total of ten naturally occurring, and hence known to be valid, sequences and two point mutants of unknown validity were used to test the usefulness of the approach. Nine of the ten valid sequences tested positive whereas both mutants tested as clearly defective. The tenth valid sequence gave results that would be interpreted as reflecting a borderline status were the answer not known. These results demonstrate that it is possible to experimentally determine which sequences in local regions of the sequence space are potentially valid 5S rRNAs. This approach will allow direct study of the constraints governing RNA evolution and allow inquiry into how the last common ancestor of extant life apparently came to have very complex ribosomal RNAs that subsequently were very conserved.

  11. Discovering novel sequence motifs with MEME.

    Science.gov (United States)

    Bailey, Timothy L

    2002-11-01

    This unit illustrates how to use MEME to discover motifs in a group of related nucleotide or peptide sequences. A MEME motif is a sequence pattern that occurs repeatedly in one or more sequences in the input group. MEME can be used to discover novel patterns because it bases its discoveries only on the input sequences, not on any prior knowledge (such as databases of known motifs). The input to MEME is a set of unaligned sequences of the same type (peptide or nucleotide). For each motif it discovers, MEME reports the occurrences (sites), consensus sequence, and the level of conservation (information content) at each position in the pattern. MEME also produces block diagrams showing where all of the discovered motifs occur in the training set sequences. MEME's hypertext (HTML) output also contains buttons that allow for the convenient use of the motifs in other searches.

  12. Design of Digital Hybrid Chaotic Sequence Generator

    Institute of Scientific and Technical Information of China (English)

    RAO Nini; ZENG Dong

    2004-01-01

    The feasibility of the hybrid chaotic sequences as the spreading codes in code divided multiple access(CDMA) system is analyzed.The design and realization of the digital hybrid chaotic sequence generator by very high speed integrated circuit hardware description language(VHDL) are described.A valid hazard canceledl method is presented.Computer simulations show that the stable digital sequence waveforms can be produced.The correlations of the digital hybrid chaotic sequences are compared with those of m-sequences.The results show that the correlations of the digital hybrid chaotic sequences are almost as good as those of m-sequences.The works in this paper explored a road for the practical applications of chaos.

  13. Sequencing technologies for animal cell culture research.

    Science.gov (United States)

    Kremkow, Benjamin G; Lee, Kelvin H

    2015-01-01

    Over the last 10 years, 2nd and 3rd generation sequencing technologies have made the use of genomic sequencing within the animal cell culture community increasingly commonplace. Each technology's defining characteristics are unique, including the cost, time, sequence read length, daily throughput, and occurrence of sequence errors. Given each sequencing technology's intrinsic advantages and disadvantages, the optimal technology for a given experiment depends on the particular experiment's objective. This review discusses the current characteristics of six next-generation sequencing technologies, compares the differences between them, and characterizes their relevance to the animal cell culture community. These technologies are continually improving, as evidenced by the recent achievement of the field's benchmark goal: sequencing a human genome for less than $1,000.

  14. "Method's Yoke": Adorno's Self-Conception as a Social Scientist and his Contribution to Qualitative Research. Two Letters from the Early Days of the "Princeton Radio Research Project"

    Directory of Open Access Journals (Sweden)

    Matthias Jung

    2013-07-01

    Full Text Available Whether or to what extent ADORNO can be regarded as a pioneer of qualitative research is discussed using two of his letters to Paul LAZARSFELD from 1938, when he began participating in the latter's "Radio Research Project" at Princeton University. In the course of the project ADORNO for the first time had to adjust to the dispositions of empirical research in the US. Due to his lack of first hand experience in this field, he had to rely on his skills as a philosopher and artist. In his correspondence with LAZARSFELD, ADORNO developed concepts that would later achieve canonical status in his writings on social research after the Second World War. By criticising quantifying methods, he naturally designed a model of qualitative research. The model nevertheless was subject to specific restrictions mainly because of ADORNO's sustained reservations regarding methodically regulated approaches in general. URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs130394

  15. Assembly Sequence Planning for Mechanical Products

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    A method for assembly sequence planning is proposed in this paper. First, two methods for assembly sequence planning are compared, which are indirect method and direct method. Then, the limits of the previous assembly planning system are pointed out. On the basis of indirect method, an improved method for assembly sequence planning is put forward. This method is composed of four parts, which are assembly modeling for products, assembly sequence representing, assembly sequence planning, and evaluation and optimization. The assembly model is established by human machine interaction, and the assembly model contains components' information and the assembly relation among the components. The assembly sequence planning is based on the breaking up of the assembly model. And/or graph is used to represent assembly sequence set. Every component which satisfies the disassembly condition is recorded as a node of an and/or graph. After the disassembly sequence and/or graph is generated, heuristic algorithm - AO* algorithm is used to search the disassembly sequence and/or graph, and the optimum assembly sequence planning is realized. This method is proved to be effective in a prototype system which is a sub-project of a state 863/CIMS research project of China - ‘Concurrent Engineering’.

  16. Randomness in Sequence Evolution Increases over Time.

    Directory of Open Access Journals (Sweden)

    Guangyu Wang

    Full Text Available The second law of thermodynamics states that entropy, as a measure of randomness in a system, increases over time. Although studies have investigated biological sequence randomness from different aspects, it remains unknown whether sequence randomness changes over time and whether this change consists with the second law of thermodynamics. To capture the dynamics of randomness in molecular sequence evolution, here we detect sequence randomness based on a collection of eight statistical random tests and investigate the randomness variation of coding sequences with an application to Escherichia coli. Given that core/essential genes are more ancient than specific/non-essential genes, our results clearly show that core/essential genes are more random than specific/non-essential genes and accordingly indicate that sequence randomness indeed increases over time, consistent well with the second law of thermodynamics. We further find that an increase in sequence randomness leads to increasing randomness of GC content and longer sequence length. Taken together, our study presents an important finding, for the first time, that sequence randomness increases over time, which may provide profound insights for unveiling the underlying mechanisms of molecular sequence evolution.

  17. Effects of an Additional Sequence of Color Stimuli on Visuomotor Sequence Learning

    Science.gov (United States)

    Tanaka, Kanji; Watanabe, Katsumi

    2017-01-01

    Through practice, people are able to integrate a secondary sequence (e.g., a stimulus-based sequence) into a primary sequence (e.g., a response-based sequence), but it is still controversial whether the integrated sequences lead to better learning than only the primary sequence. In the present study, we aimed to investigate the effects of a sequence that integrated space and color sequences on early and late learning phases (corresponding to effector-independent and effector-dependent learning, respectively) and how the effects differed in the integrated and primary sequences in each learning phase. In the task, the participants were required to learn a sequence of button presses using trial-and-error and to perform the sequence successfully for 20 trials (m × n task). First, in the baseline task, all participants learned a non-colored sequence, in which the response button always turned red. Then, in the learning task, the participants were assigned to two groups: a colored sequence group (i.e., space and color) or a non-colored sequence group (i.e., space). In the colored sequence, the response button turned a pre-determined color and the participants were instructed to attend to the sequences of both location and color as much as they could. The results showed that the participants who performed the colored sequence acquired the correct button presses of the sequence earlier, but showed a slower mean performance time than those who performed the non-colored sequence. Moreover, the slower performance time in the colored sequence group remained in a subsequent transfer task in which the spatial configurations of the buttons were vertically mirrored from the learning task. These results indicated that if participants explicitly attended to both the spatial response sequence and color stimulus sequence at the same time, they could develop their spatial representations of the sequence earlier (i.e., early development of the effector-independent learning), but might

  18. Comparison of sequence reads obtained from three next-generation sequencing platforms.

    Directory of Open Access Journals (Sweden)

    Shingo Suzuki

    Full Text Available Next-generation sequencing technologies enable the rapid cost-effective production of sequence data. To evaluate the performance of these sequencing technologies, investigation of the quality of sequence reads obtained from these methods is important. In this study, we analyzed the quality of sequence reads and SNP detection performance using three commercially available next-generation sequencers, i.e., Roche Genome Sequencer FLX System (FLX, Illumina Genome Analyzer (GA, and Applied Biosystems SOLiD system (SOLiD. A common genomic DNA sample obtained from Escherichia coli strain DH1 was applied to these sequencers. The obtained sequence reads were aligned to the complete genome sequence of E. coli DH1, to evaluate the accuracy and sequence bias of these sequence methods. We found that the fraction of "junk" data, which could not be aligned to the reference genome, was largest in the data set of SOLiD, in which about half of reads could not be aligned. Among data sets after alignment to the reference, sequence accuracy was poorest in GA data sets, suggesting relatively low fidelity of the elongation reaction in the GA method. Furthermore, by aligning the sequence reads to the E. coli strain W3110, we screened sequence differences between two E. coli strains using data sets of three different next-generation platforms. The results revealed that the detected sequence differences were similar among these three methods, while the sequence coverage required for the detection was significantly small in the FLX data set. These results provided valuable information on the quality of short sequence reads and the performance of SNP detection in three next-generation sequencing platforms.

  19. Continued fractions and heavy sequences

    CERN Document Server

    Boshernitzan, Michael

    2009-01-01

    We initiate the study of the sets $H(c)$, $0=x-[x]$ stands for the fractional part of $x\\in \\mathbb R$. We prove that, for rational $c$, the sets $H(c)$ are of positive Hausdorff dimension and, in particular, are uncountable. For integers $m\\geq1$, we obtain a surprising characterization of the numbers $\\alpha\\in H_m= H(\\frac1m)$ in terms of their continued fraction expansions: The odd entries (partial quotients) of these expansions are divisible by $m$. The characterization implies that $x\\in H_m$ if and only if $\\frac 1{mx} \\in H_m$, for $x>0$. We are unaware of a direct proof of this equivalence, without making a use of the mentioned characterization of the sets $H_m$. We also introduce the dual sets $\\hat H_m$ of reals $y$ for which the sequence of integers $\\big([ky]\\big)_{k\\geq1}$ consistently hits the set $m\\mathbb Z$ with the at least expected frequency $\\frac1m$ and establish the connection with the sets $H_m$: {2mm} If $xy=m$ for $x,y>0$, then $x\\in H_m$ if and only if $y\\in \\hat H_m$. The motivatio...

  20. Pareto optimal pairwise sequence alignment.

    Science.gov (United States)

    DeRonne, Kevin W; Karypis, George

    2013-01-01

    Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

  1. Comparison of next-generation sequencing systems.

    Science.gov (United States)

    Liu, Lin; Li, Yinhu; Li, Siliang; Hu, Ni; He, Yimin; Pong, Ray; Lin, Danni; Lu, Lihua; Law, Maggie

    2012-01-01

    With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world's biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.

  2. The genome sequence of parrot bornavirus 5.

    Science.gov (United States)

    Guo, Jianhua; Tizard, Ian

    2015-12-01

    Although several new avian bornaviruses have recently been described, information on their evolution, virulence, and sequence are often limited. Here we report the complete genome sequence of parrot bornavirus 5 (PaBV-5) isolated from a case of proventricular dilatation disease in a Palm cockatoo (Probosciger aterrimus). The complete genome consists of 8842 nucleotides with distinct 5' and 3' end sequences. This virus shares nucleotide sequence identities of 69-74 % with other bornaviruses in the genomic regions excluding the 5' and 3' terminal sequences. Phylogenetic analysis based on the genomic regions demonstrated this new isolate is an isolated branch within the clade that includes the aquatic bird bornaviruses and the passerine bornaviruses. Based on phylogenetic analyses and its low nucleotide sequence identities with other bornavirus, we support the proposal that PaBV-5 be assigned to a new bornavirus species:- Psittaciform 2 bornavirus.

  3. Application of ecostratigraphy to sequences tratigraphy

    Institute of Scientific and Technical Information of China (English)

    殷鸿福; 童金南; 张克信; 吴顺宝

    1997-01-01

    The results of ecostratigraphy can directly serve sequence stratigraphy. The habitat type curve is useful not only in the analysis of sequences and parasequences, but also in demonstration of the process of regional sea level change. The various biological surfaces usually coincide with or relate to the boundaries of sequences or system tracts. The ecostratigraphic framework composed of coenozones, community sequences and ecotracts with good timing completely corresponds to the sequence stratigraphic framework of the sedimentary basin. Therefore, through establishment of the habitat type curve in individual section, recognition of the various biological surfaces, regional ecostratigraphic correlation and the formation of an ecostratigraphic framework of the sedimentary basin, ecostratigraphy plays an important role in the study of sequence stratigraphy and the reconstruction of regional and even global sea level changes.

  4. Sequencing intractable DNA to close microbial genomes.

    Science.gov (United States)

    Hurt, Richard A; Brown, Steven D; Podar, Mircea; Palumbo, Anthony V; Elias, Dwayne A

    2012-01-01

    Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  5. Some fundamenltal problems in outcrop sequence stratigraphy

    Institute of Scientific and Technical Information of China (English)

    王训练

    1999-01-01

    Some fundamental problems in outcrop sequence stratigraphy are discussed, and the following ideas are obtained: (i) Detailed sedimentary facies analysis and study on stacking pattern of parasequences, careful and accurate study of biostratigraphy, and stratigraphical correlation of different facies areas are the essential conditions for proper identification of sequences. (ii) The first flooding surface may be an ideal sequence boundary in outcrop sequence stratigraphy, where the most distinct palaeontological and sedimentary changes take place and make the surface readily recognizable in outcrop. (iii) The distribution in space, specially in different facies belts, is regarded as an important criterion for defining and recognizing the various orders of sequences. The third-order sequence is probably global in nature , which may be discerned in various depositional facies belts at least on one continental margin, and can be correlated over long distances, sometimes worldwide. (iv) The first flooding surf

  6. Sequencing intractable DNA to close microbial genomes.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

    Full Text Available Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps and the Desulfovibrio africanus genome (1 intractable gap. The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  7. Evolutionarily conserved sequences on human chromosome 21

    Energy Technology Data Exchange (ETDEWEB)

    Frazer, Kelly A.; Sheehan, John B.; Stokowski, Renee P.; Chen, Xiyin; Hosseini, Roya; Cheng, Jan-Fang; Fodor, Stephen P.A.; Cox, David R.; Patil, Nila

    2001-09-01

    Comparison of human sequences with the DNA of other mammals is an excellent means of identifying functional elements in the human genome. Here we describe the utility of high-density oligonucleotide arrays as a rapid approach for comparing human sequences with the DNA of multiple species whose sequences are not presently available. High-density arrays representing approximately 22.5 Mb of nonrepetitive human chromosome 21 sequence were synthesized and then hybridized with mouse and dog DNA to identify sequences conserved between humans and mice (human-mouse elements) and between humans and dogs (human-dog elements). Our data show that sequence comparison of multiple species provides a powerful empiric method for identifying actively conserved elements in the human genome. A large fraction of these evolutionarily conserved elements are present in regions on chromosome 21 that do not encode known genes.

  8. Predicting Contextual Sequences via Submodular Function Maximization

    CERN Document Server

    Dey, Debadeepta; Hebert, Martial; Bagnell, J Andrew

    2012-01-01

    Sequence optimization, where the items in a list are ordered to maximize some reward has many applications such as web advertisement placement, search, and control libraries in robotics. Previous work in sequence optimization produces a static ordering that does not take any features of the item or context of the problem into account. In this work, we propose a general approach to order the items within the sequence based on the context (e.g., perceptual information, environment description, and goals). We take a simple, efficient, reduction-based approach where the choice and order of the items is established by repeatedly learning simple classifiers or regressors for each "slot" in the sequence. Our approach leverages recent work on submodular function maximization to provide a formal regret reduction from submodular sequence optimization to simple cost-sensitive prediction. We apply our contextual sequence prediction algorithm to optimize control libraries and demonstrate results on two robotics problems: ...

  9. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    DEFF Research Database (Denmark)

    de Souza, S J; Camargo, A A; Briones, M R;

    2000-01-01

    by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48......Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central...... coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1, 181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes...

  10. Preparing DNA libraries for multiplexed paired-end deep sequencing for Illumina GA sequencers.

    Science.gov (United States)

    Son, Mike S; Taylor, Ronald K

    2011-02-01

    Whole-genome sequencing, also known as deep sequencing, is becoming a more affordable and efficient way to identify SNP mutations, deletions, and insertions in DNA sequences across several different strains. Two major obstacles preventing the widespread use of deep sequencers are the costs involved in services used to prepare DNA libraries for sequencing and the overall accuracy of the sequencing data. This unit describes the preparation of DNA libraries for multiplexed paired-end sequencing using the Illumina GA series sequencer. Self-preparation of DNA libraries can help reduce overall expenses, especially if optimization is required for the different samples, and use of the Illumina GA Sequencer can improve the quality of the data.

  11. EGNAS: an exhaustive DNA sequence design algorithm

    Directory of Open Access Journals (Sweden)

    Kick Alfred

    2012-06-01

    Full Text Available Abstract Background The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences. Results The algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented. Conclusions We developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.

  12. WEAK CONVERGENCE OF HENSTOCK INTEGRABLE SEQUENCES

    Institute of Scientific and Technical Information of China (English)

    LuisaDiPiazza

    1994-01-01

    Some relationships between pointwise and weak convergence of a sequence of Henstock integrable functions are studied, In particular it is provided an example of a sequence of Henstock integrable functions whose pointwise limit is different from the weak one. By introducing an asymptotic version of the Henstock equiintegrability notion it is given a necessary and sufficient condition in order that a pointwisely convergent sequence of Henstock integrable functions is weakly convergent to its pointwise limit.

  13. Exome sequencing and genetic testing for MODY.

    Directory of Open Access Journals (Sweden)

    Stefan Johansson

    Full Text Available CONTEXT: Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when standard Sanger sequencing-based diagnostics is inconclusive. OBJECTIVE: The aim of the study was to examine the performance of exome sequencing for a molecular diagnosis of MODY in patients who have undergone conventional diagnostic sequencing of candidate genes with negative results. RESEARCH DESIGN AND METHODS: We performed exome enrichment followed by high-throughput sequencing in nine patients with suspected MODY. They were Sanger sequencing-negative for mutations in the HNF1A, HNF4A, GCK, HNF1B and INS genes. We excluded common, non-coding and synonymous gene variants, and performed in-depth analysis on filtered sequence variants in a pre-defined set of 111 genes implicated in glucose metabolism. RESULTS: On average, we obtained 45 X median coverage of the entire targeted exome and found 199 rare coding variants per individual. We identified 0-4 rare non-synonymous and nonsense variants per individual in our a priori list of 111 candidate genes. Three of the variants were considered pathogenic (in ABCC8, HNF4A and PPARG, respectively, thus exome sequencing led to a genetic diagnosis in at least three of the nine patients. Approximately 91% of known heterozygous SNPs in the target exomes were detected, but we also found low coverage in some key diabetes genes using our current exome sequencing approach. Novel variants in the genes ARAP1, GLIS3, MADD, NOTCH2 and WFS1 need further investigation to reveal their possible role in diabetes. CONCLUSION: Our results demonstrate that exome sequencing can improve molecular diagnostics of MODY when used as a complement to Sanger sequencing. However, improvements will be needed, especially concerning coverage, before the full potential of exome sequencing can be realized.

  14. cis sequence effects on gene expression

    Directory of Open Access Journals (Sweden)

    Jacobs Kevin

    2007-08-01

    Full Text Available Abstract Background Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation (genetical genomics provides insight into the role of linked sequence variation in the regulation of gene expression. We investigated the role of sequence variation in cis on gene expression (cis sequence effects in a group of genes commonly studied in cancer research in lymphoblastoid cell lines. We estimated the proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects using three different analytical approaches, and compared our results to the literature. Results We generated gene expression profiling data at N = 697 candidate genes from N = 30 lymphoblastoid cell lines for this study and used available candidate gene resequencing data at N = 552 candidate genes to identify N = 30 candidate genes with sufficient variance in both datasets for the investigation of cis sequence effects. We used two additive models and the haplotype phylogeny scanning approach of Templeton (Tree Scanning to evaluate association between individual SNPs, all SNPs at a gene, and diplotypes, with log-transformed gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p cis sequence effects in our study, respectively. Conclusion Based on analysis of our results and the extant literature, one in four genes exhibits significant cis sequence effects, and for these genes, about 30% of gene expression variation is accounted for by cis sequence variation. Despite diverse experimental approaches, the presence or absence of significant cis sequence effects is largely supported by previously published studies.

  15. Some properties of generalized Fibonacci sequence

    Science.gov (United States)

    Chong, Chin-Yoon; Ho, C. K.

    2015-12-01

    For all non-negative integer n and real constants a, b, p and q, the generalized Fibonacci sequence {U n } is defined by Un+2 = pUn+1 + qUn with the initial values U0 = a and U1 = b. Throughout the paper, we study some properties of the generalized Fibonacci sequence. Our results will motivate some new research problems concerning the contribution of the generalized sequence.

  16. Hardware Accelerated Sequence Alignment with Traceback

    Directory of Open Access Journals (Sweden)

    Scott Lloyd

    2009-01-01

    in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.

  17. Recursive sequences in first-year calculus

    Science.gov (United States)

    Krainer, Thomas

    2016-02-01

    This article provides ready-to-use supplementary material on recursive sequences for a second-semester calculus class. It equips first-year calculus students with a basic methodical procedure based on which they can conduct a rigorous convergence or divergence analysis of many simple recursive sequences on their own without the need to invoke inductive arguments as is typically required in calculus textbooks. The sequences that are accessible to this kind of analysis are predominantly (eventually) monotonic, but also certain recursive sequences that alternate around their limit point as they converge can be considered.

  18. Maize genome sequencing by methylation filtration.

    Science.gov (United States)

    Palmer, Lance E; Rabinowicz, Pablo D; O'Shaughnessy, Andrew L; Balija, Vivekanand S; Nascimento, Lidia U; Dike, Sujit; de la Bastide, Melissa; Martienssen, Robert A; McCombie, W Richard

    2003-12-19

    Gene enrichment strategies offer an alternative to sequencing large and repetitive genomes such as that of maize. We report the generation and analysis of nearly 100,000 undermethylated (or methylation filtration) maize sequences. Comparison with the rice genome reveals that methylation filtration results in a more comprehensive representation of maize genes than those that result from expressed sequence tags or transposon insertion sites sequences. About 7% of the repetitive DNA is unmethylated and thus selected in our libraries, but potentially active transposons and unmethylated organelle genomes can be identified. Reverse transcription polymerase chain reaction can be used to finish the maize transcriptome.

  19. Genomic sequencing of Pleistocene cave bears

    Energy Technology Data Exchange (ETDEWEB)

    Noonan, James P.; Hofreiter, Michael; Smith, Doug; Priest, JamesR.; Rohland, Nadin; Rabeder, Gernot; Krause, Johannes; Detter, J. Chris; Paabo, Svante; Rubin, Edward M.

    2005-04-01

    Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome, the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.

  20. Detecting Emotions from Connected Action Sequences

    Science.gov (United States)

    Bernhardt, Daniel; Robinson, Peter

    In this paper we deal with the problem of detecting emotions from the body movements produced by naturally connected action sequences. Although action sequences are one of the most common forms of body motions in everyday scenarios their potential for emotion recognition has not been explored in the past. We show that there are fundamental differences between actions recorded in isolation and in natural sequences and demonstrate a number of techniques which allow us to correctly label action sequences with one of four emotions up to 86% of the time. Our results bring us an important step closer to recognizing emotions from body movements in natural scenarios.

  1. Researches on Sequence of Plant Cystatin: Phytocystatin

    Institute of Scientific and Technical Information of China (English)

    QINQingfeng; HEWei; LIANGJun; ZHANGXingyao

    2005-01-01

    Plant cystatins or phytocystatins are cysteine proteinase inhibitors exist widely in different plant species. Because they can kill insects by inhibiting the digestive function of the cysteine proteinase in gut, they are believed to play an important role in plant's defense against pests. Phytocystatins contain the conserved QXVXG motif and show some features on their sequence different to animal cystatins.After sequencing the protein directly and the cDNA clone, a large number of plant cystatins have been characterized. A multialignment with BLAST software and a detail analysis of 38 phytocystatins show that phytocystatins possess a specific conserved amino acid sequence [LRVI]-[AGT]-[RQKE]-[FY]-[AS]-[VI]-X-[EGHDQV]-[HYFQ]-N different to the conserved sequence demonstrated by Margis in 1998. This conserved sequence can be enough to detect with exclusivity phytocystatin sequences on protein data banks. A classification of these phytocystatins is performed and they can be divided into 3 groups according to their features on amino acid sequence, and the group-I can be still divided into 3 subgroups based on the feature of their amino acid and genomic sequence. By the CLUSTALX software,the most conserved nucleotide sequences of phytocystatins were found, which could be used to design the degenerate premiers to search new phytocystatins with PCR reaction.

  2. Massively parallel sequencing of forensic STRs

    DEFF Research Database (Denmark)

    Parson, Walther; Ballard, David; Budowle, Bruce

    2016-01-01

    The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data...... accessible genome assembly, and in place before the uptake of MPS by the general forensic community starts to generate sequence data on a large scale. While the established nomenclature for CE-based STR analysis will remain unchanged in the future, the nomenclature of sequence-based STR genotypes will need...

  3. Visible periodicity of strong nucleosome DNA sequences.

    Science.gov (United States)

    Salih, Bilal; Tripathi, Vijay; Trifonov, Edward N

    2015-01-01

    Fifteen years ago, Lowary and Widom assembled nucleosomes on synthetic random sequence DNA molecules, selected the strongest nucleosomes and discovered that the TA dinucleotides in these strong nucleosome sequences often appear at 10-11 bases from one another or at distances which are multiples of this period. We repeated this experiment computationally, on large ensembles of natural genomic sequences, by selecting the strongest nucleosomes--i.e. those with such distances between like-named dinucleotides, multiples of 10.4 bases, the structural and sequence period of nucleosome DNA. The analysis confirmed the periodicity of TA dinucleotides in the strong nucleosomes, and revealed as well other periodic sequence elements, notably classical AA and TT dinucleotides. The matrices of DNA bendability and their simple linear forms--nucleosome positioning motifs--are calculated from the strong nucleosome DNA sequences. The motifs are in full accord with nucleosome positioning sequences derived earlier, thus confirming that the new technique, indeed, detects strong nucleosomes. Species- and isochore-specific variations of the matrices and of the positioning motifs are demonstrated. The strong nucleosome DNA sequences manifest the highest hitherto nucleosome positioning sequence signals, showing the dinucleotide periodicities in directly observable rather than in hidden form.

  4. Multiplexed microsatellite recovery using massively parallel sequencing.

    Science.gov (United States)

    Jennings, T N; Knaus, B J; Mullins, T D; Haig, S M; Cronn, R C

    2011-11-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356,958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5 M (USD).

  5. Locomotor sequence learning in visually guided walking.

    Science.gov (United States)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

    2016-04-01

    Voluntary limb modifications must be integrated with basic walking patterns during visually guided walking. In this study we tested whether voluntary gait modifications can become more automatic with practice. We challenged walking control by presenting visual stepping targets that instructed subjects to modify step length from one trial to the next. Our sequence learning paradigm is derived from the serial reaction-time (SRT) task that has been used in upper limb studies. Both random and ordered sequences of step lengths were used to measure sequence-specific and sequence-nonspecific learning during walking. In addition, we determined how age (i.e., healthy young adults vs. children) and biomechanical factors (i.e., walking speed) affected the rate and magnitude of locomotor sequence learning. The results showed that healthy young adults (age 24 ± 5 yr,n= 20) could learn a specific sequence of step lengths over 300 training steps. Younger children (age 6-10 yr,n= 8) had lower baseline performance, but their magnitude and rate of sequence learning were the same compared with those of older children (11-16 yr,n= 10) and healthy adults. In addition, learning capacity may be more limited at faster walking speeds. To our knowledge, this is the first study to demonstrate that spatial sequence learning can be integrated with a highly automatic task such as walking. These findings suggest that adults and children use implicit knowledge about the sequence to plan and execute leg movement during visually guided walking.

  6. A measurement of disorder in binary sequences

    Science.gov (United States)

    Gong, Longyan; Wang, Haihong; Cheng, Weiwen; Zhao, Shengmei

    2015-03-01

    We propose a complex quantity, AL, to characterize the degree of disorder of L-length binary symbolic sequences. As examples, we respectively apply it to typical random and deterministic sequences. One kind of random sequences is generated from a periodic binary sequence and the other is generated from the logistic map. The deterministic sequences are the Fibonacci and Thue-Morse sequences. In these analyzed sequences, we find that the modulus of AL, denoted by |AL | , is a (statistically) equivalent quantity to the Boltzmann entropy, the metric entropy, the conditional block entropy and/or other quantities, so it is a useful quantitative measure of disorder. It can be as a fruitful index to discern which sequence is more disordered. Moreover, there is one and only one value of |AL | for the overall disorder characteristics. It needs extremely low computational costs. It can be easily experimentally realized. From all these mentioned, we believe that the proposed measure of disorder is a valuable complement to existing ones in symbolic sequences.

  7. Strebel differentials and Hamilton sequences

    Institute of Scientific and Technical Information of China (English)

    LI; Zhong(

    2001-01-01

    [1]Strebel, K., Point shift differentials and extremal quasiconformal mappings, Annale Acad. Scle. Fenn. Math., 1998, 23: 475 -494.[2]Gardiner, F. P., Approximation of infinite dimensional Teichmutller space, Trans. Amer. Soc., 1999, 282: 367-383.[3]Lakic, N. , The Strebel points, Comptemp. Math. , 1997, 211: 417-431.[4]Wu Sheng jian, Hamilton sequences for extremal quasiconformal mappings of the unit disc, Science in China, Ser. A, 1999,42(10): 1033-1042.[5]Li Zhong, Qi Yi, A note on point shift differentials, Science in China, Ser. A, 1999, 42(5): 449-455.[6]Hamilton, R. S., Extremal quasiconformal mappings with prescribed boundary values, Trans. Amer. Math. Soc. , 1969,138: 399-406.[7]Krushkal, S. , Extremal quasiconformal mappings, Sirbirsk. Mat. Zh., 1969, 10: 573-583.[8]Reich, E., Strebel, K., Extremal quasiconformal mappings with given boundary values, Contributions to Analysis, New York: Academic Press, 1974, 375-391.[9]Strebel, K. , On quasiconformal mappings of open Riemann surfaces, Commemt. Math. Helr., 1978, 53: 301-321.[10]Earle, C., Li Zhong, Extremal quasiconformal mappings in plane domains, Quasiconformal Mappings and Analysis A Col-lection of Papers Honoring F. W. Gehring, New York: Springer-Verlag, 1998, 141-158.[11]Strebel, K., On quadratic differentials and extremal quasiconforrnal mappings, in Proc. of the Intern. Congress of Math.,Vancouver, 1974.[12]Li Zhong, Some new results on the geometry of infinite dimensional Teichmuller space, in Proceedings of the 3rd International Colloquium on Finite or Infinite Dimensional Complex Analysis, 1995, 369-378.

  8. Compressing DNA sequence databases with coil

    Directory of Open Access Journals (Sweden)

    Hendy Michael D

    2008-05-01

    Full Text Available Abstract Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

  9. Timing-Sequence Testing of Parallel Programs

    Institute of Scientific and Technical Information of China (English)

    LIANG Yu; LI Shu; ZHANG Hui; HAN Chengde

    2000-01-01

    Testing of parallel programs involves two parts-testing of controlflow within the processes and testing of timing-sequence.This paper focuses on the latter, particularly on the timing-sequence of message-passing paradigms.Firstly the coarse-grained SYN-sequence model is built up to describe the execution of distributed programs. All of the topics discussed in this paper are based on it. The most direct way to test a program is to run it. A fault-free parallel program should be of both correct computing results and proper SYN-sequence. In order to analyze the validity of observed SYN-sequence, this paper presents the formal specification (Backus Normal Form) of the valid SYN-sequence. Till now there is little work about the testing coverage for distributed programs. Calculating the number of the valid SYN-sequences is the key to coverage problem, while the number of the valid SYN-sequences is terribly large and it is very hard to obtain the combination law among SYN-events. In order to resolve this problem, this paper proposes an efficient testing strategy-atomic SYN-event testing, which is to linearize the SYN-sequence (making it only consist of serial atomic SYN-events) first and then test each atomic SYN-event independently. This paper particularly provides the calculating formula about the number of the valid SYN-sequences for tree-topology atomic SYN-event (broadcast and combine). Furthermore,the number of valid SYN-sequences also,to some degree, mirrors the testability of parallel programs. Taking tree-topology atomic SYN-event as an example, this paper demonstrates the testability and communication speed of the tree-topology atomic SYN-event under different numbers of branches in order to achieve a more satisfactory tradeoff between testability and communication efficiency.

  10. Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

    Directory of Open Access Journals (Sweden)

    Marta Brozynska

    Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

  11. Generalized Identities of Companion Fibonacci-Like Sequences

    OpenAIRE

    Shikha Bhatnagar; Bijendra Singh; Omprakash Sikhwal

    2013-01-01

    The Fibonacci sequence, Lucas sequence, Pell sequence, Pell-Lucas sequence, Jacobsthalsequence and Jacobsthal-Lucas sequence are most prominent examples of second order recursivesequences. In this paper, we deal with two companion Fibonacci- Like sequences which aregeneralization of Fibonacci-Like sequence. Further we obtain some generalized identities amongthe terms of companion Fibonacci-Like sequences, Jacobsthal and Jacobsthal-Lucas sequencesthrough Binet’s formulae.

  12. Sequencing the Cotton Genomes-Gossypium spp.

    Institute of Scientific and Technical Information of China (English)

    PATERSON Andrew H

    2008-01-01

    @@ The genomes of most major crops,including cotton,will be fully sequenced in the next fewyears.Cotton is unusual,although not unique,in that we will need to sequence not only cultivated(tetraploid) genotypes but their diploid progenitors,to understand how elite cottons have surpassedthe productivity and quality of their progenitors.

  13. Convergence of a Linear Recursive Sequence

    Science.gov (United States)

    Tay, E. G.; Toh, T. L.; Dong, F. M.; Lee, T. Y.

    2004-01-01

    A necessary and sufficient condition is found for a linear recursive sequence to be convergent, no matter what initial values are given. Its limit is also obtained when the sequence is convergent. Methods from various areas of mathematics are used to obtain the results.

  14. Novel algorithms for protein sequence analysis

    NARCIS (Netherlands)

    Ye, Kai

    2008-01-01

    Each protein is characterized by its unique sequential order of amino acids, the so-called protein sequence. Biology”s paradigm is that this order of amino acids determines the protein”s architecture and function. In this thesis, we introduce novel algorithms to analyze protein sequences. Chapter 1

  15. Sequencing for the cream of the crop

    Science.gov (United States)

    In this invited commentary, we discuss how next-generation sequencing methods are beginning to find their way into plant genetics, promising substantial improvements in crop yields over the coming decades. Next-generation sequencing facilitates the construction of high-resolution variation maps, whi...

  16. Sequencing Events: Exploring Art and Art Jobs.

    Science.gov (United States)

    Stephens, Pamela Geiger; Shaddix, Robin K.

    2000-01-01

    Presents an activity for upper-elementary students that correlates the actions of archaeologists, patrons, and artists with the sequencing of events in a logical order. Features ancient Egyptian art images. Discusses the preparation of materials, motivation, a pre-writing activity, and writing a story in sequence. (CMK)

  17. Pig genome sequence - analysis and publication strategy

    DEFF Research Database (Denmark)

    Archibald, Alan L.; Bolund, Lars; Churcher, Carol

    2010-01-01

    preferentially selected for sequencing. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement the data have been released into public sequence repositories (Genbank/EMBL, NCBI/Ensembl trace repositories) in a timely manner and in advance of publication. CONCLUSIONS...

  18. Sequence Comparison: Close and Open problems

    NARCIS (Netherlands)

    Lenzini, Gabriele; Cerrai, P.; Freguglia, P.

    1997-01-01

    Comparing sequences is a very important activity both in computer science and in a many other areas as well. For example thank to text editors, everyone knows the particular instance of a sequence comparison problem knonw as ``string mathcing problem''. It consists in searching a given work eventual

  19. Stochastic modelling of daily rainfall sequences

    NARCIS (Netherlands)

    Buishand, T.A.

    1977-01-01

    Rainfall series of different climatic regions were analysed with the aim of generating daily rainfall sequences. A survey of the data is given in I, 1. When analysing daily rainfall sequences one must be aware of the following points:
    a. Seasonality. Because of seasonal variation

  20. Genome Sequence of Lactobacillus rhamnosus ATCC 8530

    OpenAIRE

    Pittet, Vanessa; Ewen, Emily; Bushell, Barry R.; Ziola, Barry

    2012-01-01

    Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available L. rhamnosus genome sequences.

  1. SEQUENCE IN LEARNING--FACT OR FICTION.

    Science.gov (United States)

    MIEL, ALICE

    SEQUENCE IN LEARNING IS USEFUL ONLY AS IT CONTRIBUTES TO THE CONTINUITY OF A CHILD'S OVERALL DEVELOPMENT. CHILDREN MAY NOT GO THROUGH THE SAME SEQUENCE TO ARRIVE AT A SIMILAR POINT OF UNDERSTANDING. EDUCATIONAL PROGRESS IS INDICATED BY A CHILD'S GROWTH IN THE DEVELOPMENT OF STRATEGIC CONCEPTS, IN WAYS OF PROCESSING INFORMATION, AND IN WAYS OF…

  2. Controlling monomer-sequence using supramolecular templates

    OpenAIRE

    ten Brummelhuis, Niels

    2014-01-01

    The transcription and translation of information contained in nucleic acids that has been perfected by nature serves as inspiration for chemists to devise strategies for the creation of polymers with welldefined monomer sequences. In this review the various approaches in which templates (either biopolymers or synthetic ones) are used to influence the monomer-sequence are discussed.

  3. What's Next? Judging Sequences of Binary Events

    Science.gov (United States)

    Oskarsson, An T.; Van Boven, Leaf; McClelland, Gary H.; Hastie, Reid

    2009-01-01

    The authors review research on judgments of random and nonrandom sequences involving binary events with a focus on studies documenting gambler's fallacy and hot hand beliefs. The domains of judgment include random devices, births, lotteries, sports performances, stock prices, and others. After discussing existing theories of sequence judgments,…

  4. SPARSE SEQUENCE CONSTRUCTION OF LDPC CODES

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    This letter proposes a novel and simple construction of regular Low-Density Parity-Check (LDPC) codes using sparse binary sequences. It utilizes the cyclic cross correlation function of sparse sequences to generate codes with girth8. The new codes perform well using the sumproduct decoding. Low encodingcomplexity can also be achieved due to the inherent quasi-cyclic structure of the codes.

  5. Sequence Comparison: Close and Open problems

    NARCIS (Netherlands)

    Lenzini, Gabriele; Cerrai, P.; Freguglia, P.

    Comparing sequences is a very important activity both in computer science and in a many other areas as well. For example thank to text editors, everyone knows the particular instance of a sequence comparison problem knonw as ``string mathcing problem''. It consists in searching a given work

  6. Archaebacterial rhodopsin sequences: Implications for evolution

    Science.gov (United States)

    Lanyi, J. K.

    1991-01-01

    It was proposed over 10 years ago that the archaebacteria represent a separate kingdom which diverged very early from the eubacteria and eukaryotes. It follows that investigations of archaebacterial characteristics might reveal features of early evolution. So far, two genes, one for bacteriorhodopsin and another for halorhodopsin, both from Halobacterium halobium, have been sequenced. We cloned and sequenced the gene coding for the polypeptide of another one of these rhodopsins, a halorhodopsin in Natronobacterium pharaonis. Peptide sequencing of cyanogen bromide fragments, and immuno-reactions of the protein and synthetic peptides derived from the C-terminal gene sequence, confirmed that the open reading frame was the structural gene for the pharaonis halorhodopsin polypeptide. The flanking DNA sequences of this gene, as well as those of other bacterial rhodopsins, were compared to previously proposed archaebacterial consensus sequences. In pairwise comparisons of the open reading frame with DNA sequences for bacterio-opsin and halo-opsin from Halobacterium halobium, silent divergences were calculated. These indicate very considerable evolutionary distance between each pair of genes, even in the dame organism. In spite of this, three protein sequences show extensive similarities, indicating strong selective pressures.

  7. Bonobos extract meaning from call sequences.

    Directory of Open Access Journals (Sweden)

    Zanna Clay

    Full Text Available Studies on language-trained bonobos have revealed their remarkable abilities in representational and communication tasks. Surprisingly, however, corresponding research into their natural communication has largely been neglected. We address this issue with a first playback study on the natural vocal behaviour of bonobos. Bonobos produce five acoustically distinct call types when finding food, which they regularly mix together into longer call sequences. We found that individual call types were relatively poor indicators of food quality, while context specificity was much greater at the call sequence level. We therefore investigated whether receivers could extract meaning about the quality of food encountered by the caller by integrating across different call sequences. We first trained four captive individuals to find two types of foods, kiwi (preferred and apples (less preferred at two different locations. We then conducted naturalistic playback experiments during which we broadcasted sequences of four calls, originally produced by a familiar individual responding to either kiwi or apples. All sequences contained the same number of calls but varied in the composition of call types. Following playbacks, we found that subjects devoted significantly more search effort to the field indicated by the call sequence. Rather than attending to individual calls, bonobos attended to the entire sequences to make inferences about the food encountered by a caller. These results provide the first empirical evidence that bonobos are able to extract information about external events by attending to vocal sequences of other individuals and highlight the importance of call combinations in their natural communication system.

  8. What's Next? Judging Sequences of Binary Events

    Science.gov (United States)

    Oskarsson, An T.; Van Boven, Leaf; McClelland, Gary H.; Hastie, Reid

    2009-01-01

    The authors review research on judgments of random and nonrandom sequences involving binary events with a focus on studies documenting gambler's fallacy and hot hand beliefs. The domains of judgment include random devices, births, lotteries, sports performances, stock prices, and others. After discussing existing theories of sequence judgments,…

  9. Wolbachia Sequence Typing in Butterflies Using Pyrosequencing.

    Science.gov (United States)

    Choi, Sungmi; Shin, Su-Kyoung; Jeong, Gilsang; Yi, Hana

    2015-09-01

    Wolbachia is an obligate symbiotic bacteria that is ubiquitous in arthropods, with 25-70% of insect species estimated to be infected. Wolbachia species can interact with their insect hosts in a mutualistic or parasitic manner. Sequence types (ST) of Wolbachia are determined by multilocus sequence typing (MLST) of housekeeping genes. However, there are some limitations to MLST with respect to the generation of clone libraries and the Sanger sequencing method when a host is infected with multiple STs of Wolbachia. To assess the feasibility of massive parallel sequencing, also known as next-generation sequencing, we used pyrosequencing for sequence typing of Wolbachia in butterflies. We collected three species of butterflies (Eurema hecabe, Eurema laeta, and Tongeia fischeri) common to Korea and screened them for Wolbachia STs. We found that T. fischeri was infected with a single ST of Wolbachia, ST41. In contrast, E. hecabe and E. laeta were each infected with two STs of Wolbachia, ST41 and ST40. Our results clearly demonstrate that pyrosequencing-based MLST has a higher sensitivity than cloning and Sanger sequencing methods for the detection of minor alleles. Considering the high prevalence of infection with multiple Wolbachia STs, next-generation sequencing with improved analysis would assist with scaling up approaches to Wolbachia MLST.

  10. Value of a newly sequenced bacterial genome

    DEFF Research Database (Denmark)

    Barbosa, Eudes; Aburjaile, Flavia F; Ramos, Rommel Tj

    2014-01-01

    and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses...

  11. Discrepancy of LS-sequences of partitions

    CERN Document Server

    Carbone, Ingrid

    2010-01-01

    In this paper we give a precise estimate of the discrepancy of a class of uniformly distributed sequences of partitions. Among them we found a large class having low discrepancy (which means of order 1/N. One of them is the Kakutani-Fibonacci sequence.

  12. Some identities of generalized Fibonacci sequence

    Science.gov (United States)

    Chong, Chin-Yoon; Cheah, C. L.; Ho, C. K.

    2014-07-01

    We introduced the generalized Fibonacci sequence {Un} defined by U0 = 0, U1 = 1, and Un+2 = pUn+1+qUn for all p, q∈Z+ and for all non-negative integers n. In this paper, we obtained some recursive formulas of the sequence.

  13. On the sum of generalized Fibonacci sequence

    Science.gov (United States)

    Chong, Chin-Yoon; Ho, C. K.

    2014-06-01

    We consider the generalized Fibonacci sequence {Un defined by U0 = 0, U1 = 1, and Un+2 = pUn+1+qUn for all n∈Z0+ and p, q∈Z+. In this paper, we derived various sums of the generalized Fibonacci sequence from their recursive relations.

  14. Regular Pentagons and the Fibonacci Sequence.

    Science.gov (United States)

    French, Doug

    1989-01-01

    Illustrates how to draw a regular pentagon. Shows the sequence of a succession of regular pentagons formed by extending the sides. Calculates the general formula of the Lucas and Fibonacci sequences. Presents a regular icosahedron as an example of the golden ratio. (YP)

  15. GENE SEQUENCE HOMOLOGY OF CHEMOKINES ACROSS SPECIES

    Science.gov (United States)

    The abundance of expressed gene and protein sequences available in the biological information databases facilitates comparison of protein homologies. A high degree of sequence similarity typically implies homology regarding structure and function and may provide clues to antibody cross-react...

  16. Concept For Generation Of Long Pseudorandom Sequences

    Science.gov (United States)

    Wang, C. C.

    1990-01-01

    Conceptual very-large-scale integrated (VLSI) digital circuit performs exponentiation in finite field. Algorithm that generates unusually long sequences of pseudorandom numbers executed by digital processor that includes such circuits. Concepts particularly advantageous for such applications as spread-spectrum communications, cryptography, and generation of ranging codes, synthetic noise, and test data, where usually desirable to make pseudorandom sequences as long as possible.

  17. Using Conventional Sequences in L2 French

    Science.gov (United States)

    Forsberg, Fanny

    2010-01-01

    By means of a phraseological identification method, this study provides a general description of the use of conventional sequences (CSs) in interviews at four different levels of spoken L2 French as well as in interviews with native speakers. Use of conventional sequences is studied with regard to overall quantity, category distribution and type…

  18. Fibonacci-triple sequences and some fundamental properties

    Directory of Open Access Journals (Sweden)

    Bijendra Singh

    2010-12-01

    Full Text Available Fibonacci sequence stands as a kind of super sequence with fabulous properties. This note presents Fibonacci-Triple sequences that may also be called 3-F sequences. This is the explosive development in the region of Fibonacci sequence. Our purpose of this paper is to demonstrate fundamental properties of Fibonacci-Triple sequence.

  19. Fibonacci-triple sequences and some fundamental properties

    OpenAIRE

    Bijendra Singh; Omprakash Sikhwal

    2010-01-01

    Fibonacci sequence stands as a kind of super sequence with fabulous properties. This note presents Fibonacci-Triple sequences that may also be called 3-F sequences. This is the explosive development in the region of Fibonacci sequence. Our purpose of this paper is to demonstrate fundamental properties of Fibonacci-Triple sequence.

  20. Conserved Sequence Processing in Primate Frontal Cortex.

    Science.gov (United States)

    Wilson, Benjamin; Marslen-Wilson, William D; Petkov, Christopher I

    2017-02-01

    An important aspect of animal perception and cognition is learning to recognize relationships between environmental events that predict others in time, a form of relational knowledge that can be assessed using sequence-learning paradigms. Humans are exquisitely sensitive to sequencing relationships, and their combinatorial capacities, most saliently in the domain of language, are unparalleled. Recent comparative research in human and nonhuman primates has obtained behavioral and neuroimaging evidence for evolutionarily conserved substrates involved in sequence processing. The findings carry implications for the origins of domain-general capacities underlying core language functions in humans. Here, we synthesize this research into a 'ventrodorsal gradient' model, where frontal cortex engagement along this axis depends on sequencing complexity, mapping onto the sequencing capacities of different species. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Sequencing and comparing whole mitochondrial genomes ofanimals

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  2. NGS-based deep bisulfite sequencing.

    Science.gov (United States)

    Lee, Suman; Kim, Joomyeong

    2016-01-01

    We have developed an NGS-based deep bisulfite sequencing protocol for the DNA methylation analysis of genomes. This approach allows the rapid and efficient construction of NGS-ready libraries with a large number of PCR products that have been individually amplified from bisulfite-converted DNA. This approach also employs a bioinformatics strategy to sort the raw sequence reads generated from NGS platforms and subsequently to derive DNA methylation levels for individual loci. The results demonstrated that this NGS-based deep bisulfite sequencing approach provide not only DNA methylation levels but also informative DNA methylation patterns that have not been seen through other existing methods.•This protocol provides an efficient method generating NGS-ready libraries from individually amplified PCR products.•This protocol provides a bioinformatics strategy sorting NGS-derived raw sequence reads.•This protocol provides deep bisulfite sequencing results that can measure DNA methylation levels and patterns of individual loci.

  3. Locomotor sequence learning in visually guided walking

    DEFF Research Database (Denmark)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

    2016-01-01

    walking. In addition, we determined how age (i.e., healthy young adults vs. children) and biomechanical factors (i.e., walking speed) affected the rate and magnitude of locomotor sequence learning. The results showed that healthy young adults (age 24 ± 5 years, N = 20) could learn a specific sequence...... of step lengths over 300 training steps. Younger children (age 6-10 years, N = 8) have lower baseline performance, but their magnitude and rate of sequence learning was the same compared to older children (11-16 years, N = 10) and healthy adults. In addition, learning capacity may be more limited...... at faster walking speeds. To our knowledge, this is the first study to demonstrate that spatial sequence learning can be integrated with a highly automatic task like walking. These findings suggest that adults and children use implicit knowledge about the sequence to plan and execute leg movement during...

  4. Spiking neuron model for temporal sequence recognition.

    Science.gov (United States)

    Byrnes, Sean; Burkitt, Anthony N; Grayden, David B; Meffin, Hamish

    2010-01-01

    A biologically inspired neuronal network that stores and recognizes temporal sequences of symbols is described. Each symbol is represented by excitatory input to distinct groups of neurons (symbol pools). Unambiguous storage of multiple sequences with common subsequences is ensured by partitioning each symbol pool into subpools that respond only when the current symbol has been preceded by a particular sequence of symbols. We describe synaptic structure and neural dynamics that permit the selective activation of subpools by the correct sequence. Symbols may have varying durations of the order of hundreds of milliseconds. Physiologically plausible plasticity mechanisms operate on a time scale of tens of milliseconds; an interaction of the excitatory input with periodic global inhibition bridges this gap so that neural events representing successive symbols occur on this much faster timescale. The network is shown to store multiple overlapping sequences of events. It is robust to variation in symbol duration, it is scalable, and its performance degrades gracefully with perturbation of its parameters.

  5. Aligning Sequences by Minimum Description Length

    Directory of Open Access Journals (Sweden)

    John S. Conery

    2008-01-01

    Full Text Available This paper presents a new information theoretic framework for aligning sequences in bioinformatics. A transmitter compresses a set of sequences by constructing a regular expression that describes the regions of similarity in the sequences. To retrieve the original set of sequences, a receiver generates all strings that match the expression. An alignment algorithm uses minimum description length to encode and explore alternative expressions; the expression with the shortest encoding provides the best overall alignment. When two substrings contain letters that are similar according to a substitution matrix, a code length function based on conditional probabilities defined by the matrix will encode the substrings with fewer bits. In one experiment, alignments produced with this new method were found to be comparable to alignments from CLUSTALW. A second experiment measured the accuracy of the new method on pairwise alignments of sequences from the BAliBASE alignment benchmark.

  6. Metagenomics using next-generation sequencing.

    Science.gov (United States)

    Bragg, Lauren; Tyson, Gene W

    2014-01-01

    Traditionally, microbial genome sequencing has been restricted to the small number of species that can be grown in pure culture. The progressive development of culture-independent methods over the last 15 years now allows researchers to sequence microbial communities directly from environmental samples. This approach is commonly referred to as "metagenomics" or "community genomics". However, the term metagenomics is applied liberally in the literature to describe any culture-independent analysis of microbial communities. Here, we define metagenomics as shotgun ("random") sequencing of the genomic DNA of a sample taken directly from the environment. The metagenome can be thought of as a sampling of the collective genome of the microbial community. We outline the considerations and analyses that should be undertaken to ensure the success of a metagenomic sequencing project, including the choice of sequencing platform and methods for assembly, binning, annotation, and comparative analysis.

  7. Strategies for complete plastid genome sequencing.

    Science.gov (United States)

    Twyford, Alex D; Ness, Rob W

    2016-10-28

    Plastid sequencing is an essential tool in the study of plant evolution. This high-copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low-cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation-sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly. These developments allow for a much more streamlined assembly than via conventional short-range PCR. Although newer methods make complete plastid sequencing possible for any land plant or green alga, there are still challenges for producing finished plastomes particularly from herbarium material or from structurally divergent plastids such as those of parasitic plants.

  8. Reading biological processes from nucleotide sequences

    Science.gov (United States)

    Murugan, Anand

    Cellular processes have traditionally been investigated by techniques of imaging and biochemical analysis of the molecules involved. The recent rapid progress in our ability to manipulate and read nucleic acid sequences gives us direct access to the genetic information that directs and constrains biological processes. While sequence data is being used widely to investigate genotype-phenotype relationships and population structure, here we use sequencing to understand biophysical mechanisms. We present work on two different systems. First, in chapter 2, we characterize the stochastic genetic editing mechanism that produces diverse T-cell receptors in the human immune system. We do this by inferring statistical distributions of the underlying biochemical events that generate T-cell receptor coding sequences from the statistics of the observed sequences. This inferred model quantitatively describes the potential repertoire of T-cell receptors that can be produced by an individual, providing insight into its potential diversity and the probability of generation of any specific T-cell receptor. Then in chapter 3, we present work on understanding the functioning of regulatory DNA sequences in both prokaryotes and eukaryotes. Here we use experiments that measure the transcriptional activity of large libraries of mutagenized promoters and enhancers and infer models of the sequence-function relationship from this data. For the bacterial promoter, we infer a physically motivated 'thermodynamic' model of the interaction of DNA-binding proteins and RNA polymerase determining the transcription rate of the downstream gene. For the eukaryotic enhancers, we infer heuristic models of the sequence-function relationship and use these models to find synthetic enhancer sequences that optimize inducibility of expression. Both projects demonstrate the utility of sequence information in conjunction with sophisticated statistical inference techniques for dissecting underlying biophysical

  9. GASP: Gapped Ancestral Sequence Prediction for proteins

    Directory of Open Access Journals (Sweden)

    Shields Denis C

    2004-09-01

    Full Text Available Abstract Background The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate alignments and phylogenies. Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel events or sequence fragments. Results Here we present a new algorithm, GASP (Gapped Ancestral Sequence Prediction, for predicting ancestral sequences from phylogenetic trees and the corresponding multiple sequence alignments. Alignments may be of any size and contain gaps. GASP first assigns the positions of gaps in the phylogeny before using a likelihood-based approach centred on amino acid substitution matrices to assign ancestral amino acids. Important outgroup information is used by first working down from the tips of the tree to the root, using descendant data only to assign probabilities, and then working back up from the root to the tips using descendant and outgroup data to make predictions. GASP was tested on a number of simulated datasets based on real phylogenies. Prediction accuracy for ungapped data was similar to three alternative algorithms tested, with GASP performing better in some cases and worse in others. Adding simple insertions and deletions to the simulated data did not have a detrimental effect on GASP accuracy. Conclusions GASP (Gapped Ancestral Sequence Prediction will predict ancestral sequences from multiple protein alignments of any size. Although not as accurate in all cases as some of the more sophisticated maximum likelihood approaches, it can process a wide range of input phylogenies and will predict ancestral sequences for gapped and ungapped residues alike.

  10. GASP: Gapped Ancestral Sequence Prediction for proteins.

    Science.gov (United States)

    Edwards, Richard J; Shields, Denis C

    2004-09-06

    The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate alignments and phylogenies. Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel) events or sequence fragments. Here we present a new algorithm, GASP (Gapped Ancestral Sequence Prediction), for predicting ancestral sequences from phylogenetic trees and the corresponding multiple sequence alignments. Alignments may be of any size and contain gaps. GASP first assigns the positions of gaps in the phylogeny before using a likelihood-based approach centred on amino acid substitution matrices to assign ancestral amino acids. Important outgroup information is used by first working down from the tips of the tree to the root, using descendant data only to assign probabilities, and then working back up from the root to the tips using descendant and outgroup data to make predictions. GASP was tested on a number of simulated datasets based on real phylogenies. Prediction accuracy for ungapped data was similar to three alternative algorithms tested, with GASP performing better in some cases and worse in others. Adding simple insertions and deletions to the simulated data did not have a detrimental effect on GASP accuracy. GASP (Gapped Ancestral Sequence Prediction) will predict ancestral sequences from multiple protein alignments of any size. Although not as accurate in all cases as some of the more sophisticated maximum likelihood approaches, it can process a wide range of input phylogenies and will predict ancestral sequences for gapped and ungapped residues alike.

  11. On some difference sequence spaces defined by a sequence of Orlicz functions

    Institute of Scientific and Technical Information of China (English)

    ASMA BEKTA(S) (C)i(g)dem

    2006-01-01

    The idea of difference sequence spaces was introduced in (Kizmaz, 1981) and this concept was generalized in (Et and Colak, 1995). In this paper we define some difference sequence spaces by a sequence of Orlicz functions and establish some inclusion relations.

  12. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

    Science.gov (United States)

    Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

    2017-07-01

    PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

  13. Finding Common Sequence and Structure Motifs in a set of RNA sequences

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Heyer, Laurie J.; Stormo, Gary D.

    1997-01-01

    We present a computational scheme to search for the most common motif, composed of a combination of sequence and structure constraints, among a collection of RNA sequences. The method uses a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences...

  14. SOME GEOMETRIC PROPERTIES OF A NEW DIFFERENCE SEQUENCE SPACE INVOLVING LACUNARY SEQUENCES

    Institute of Scientific and Technical Information of China (English)

    Murat KARAKAŞ; Mikail ET; Vatan KARAKAYA

    2013-01-01

    In this paper, we define a new generalized difference sequence space involving lacunary sequence. Then, we examine k-NUC property and property (β) for this space and also show that it is not rotund where p=(pr) is a bounded sequence of positive real numbers with pr ≥1 for all r∈N.

  15. Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics

    NARCIS (Netherlands)

    Sikkema-Raddatz, B.; Johansson, L.F.; de Boer, E.N.; Almomani, R.; Boven, L.G.; van den Berg, M.P.; van Spaendonck-Zwarts, K.Y.; van Tintelen, J.P.; Sijmons, R.H.; Jongbloed, J.D.H.; Sinke, R.J.

    2013-01-01

    Mutation detection through exome sequencing allows simultaneous analysis of all coding sequences of genes. However, it cannot yet replace Sanger sequencing (SS) in diagnostics because of incomplete representation and coverage of exons leading to missing clinically relevant mutations. Targeted next-g

  16. Sequencing and Analysis of a Genomic Fragment Provide an Insight into the Dunaliella viridis Genomic Sequence

    Institute of Scientific and Technical Information of China (English)

    Xiao-Ming SUN; Yuan-Ping TANG; Xiang-Zong MENG; Wen-Wen ZHANG; Shan LI; Zhi-Rui DENG; Zheng-Kai XU; Ren-Tao SONG

    2006-01-01

    Dunaliella is a genus of wall-less unicellular eukaryotic green alga. Its exceptional resistances to salt and various other stresses have made it an ideal model for stress tolerance study. However, very little is known about its genome and genomic sequences. In this study, we sequenced and analyzed a 29,268 bp genomic fragment from Dunaliella viridis. The fragment showed low sequence homology to the GenBank database. At the nucleotide level, only a segment with significant sequence homology to 18S rRNA was found. The fragment contained six putative genes, but only one gene showed significant homology at the protein level to GenBank database. The average GC content of this sequence was 51.1%, which was much lower than that of close related green algae Chlamydomonas (65.7%). Significant segmental duplications were found within this fragment. The duplicated sequences accounted for about 35.7% of the entire region. Large amounts of simple sequence repeats (microsatellites) were found, with strong bias towards (AC)n type (76%). Analysis of other Dunaliella genomic sequences in the GenBank database (total 25,749 bp) was in agreement with these findings. These sequence features made it difficult to sequence Dunaliella genomic sequences. Further investigation should be made to reveal the biological significance of these unique sequence features.

  17. Gelada vocal sequences follow Menzerath's linguistic law.

    Science.gov (United States)

    Gustison, Morgan L; Semple, Stuart; Ferrer-I-Cancho, Ramon; Bergman, Thore J

    2016-05-10

    Identifying universal principles underpinning diverse natural systems is a key goal of the life sciences. A powerful approach in addressing this goal has been to test whether patterns consistent with linguistic laws are found in nonhuman animals. Menzerath's law is a linguistic law that states that, the larger the construct, the smaller the size of its constituents. Here, to our knowledge, we present the first evidence that Menzerath's law holds in the vocal communication of a nonhuman species. We show that, in vocal sequences of wild male geladas (Theropithecus gelada), construct size (sequence size in number of calls) is negatively correlated with constituent size (duration of calls). Call duration does not vary significantly with position in the sequence, but call sequence composition does change with sequence size and most call types are abbreviated in larger sequences. We also find that intercall intervals follow the same relationship with sequence size as do calls. Finally, we provide formal mathematical support for the idea that Menzerath's law reflects compression-the principle of minimizing the expected length of a code. Our findings suggest that a common principle underpins human and gelada vocal communication, highlighting the value of exploring the applicability of linguistic laws in vocal systems outside the realm of language.

  18. De novo peptide sequencing by deep learning.

    Science.gov (United States)

    Tran, Ngoc Hieu; Zhang, Xianglilan; Xin, Lei; Shan, Baozhen; Li, Ming

    2017-07-18

    De novo peptide sequencing from tandem MS data is the key technology in proteomics for the characterization of proteins, especially for new sequences, such as mAbs. In this study, we propose a deep neural network model, DeepNovo, for de novo peptide sequencing. DeepNovo architecture combines recent advances in convolutional neural networks and recurrent neural networks to learn features of tandem mass spectra, fragment ions, and sequence patterns of peptides. The networks are further integrated with local dynamic programming to solve the complex optimization task of de novo sequencing. We evaluated the method on a wide variety of species and found that DeepNovo considerably outperformed state of the art methods, achieving 7.7-22.9% higher accuracy at the amino acid level and 38.1-64.0% higher accuracy at the peptide level. We further used DeepNovo to automatically reconstruct the complete sequences of antibody light and heavy chains of mouse, achieving 97.5-100% coverage and 97.2-99.5% accuracy, without assisting databases. Moreover, DeepNovo is retrainable to adapt to any sources of data and provides a complete end-to-end training and prediction solution to the de novo sequencing problem. Not only does our study extend the deep learning revolution to a new field, but it also shows an innovative approach in solving optimization problems by using deep learning and dynamic programming.

  19. Fungal genome sequencing: basic biology to biotechnology.

    Science.gov (United States)

    Sharma, Krishna Kant

    2016-08-01

    The genome sequences provide a first glimpse into the genomic basis of the biological diversity of filamentous fungi and yeast. The genome sequence of the budding yeast, Saccharomyces cerevisiae, with a small genome size, unicellular growth, and rich history of genetic and molecular analyses was a milestone of early genomics in the 1990s. The subsequent completion of fission yeast, Schizosaccharomyces pombe and genetic model, Neurospora crassa initiated a revolution in the genomics of the fungal kingdom. In due course of time, a substantial number of fungal genomes have been sequenced and publicly released, representing the widest sampling of genomes from any eukaryotic kingdom. An ambitious genome-sequencing program provides a wealth of data on metabolic diversity within the fungal kingdom, thereby enhancing research into medical science, agriculture science, ecology, bioremediation, bioenergy, and the biotechnology industry. Fungal genomics have higher potential to positively affect human health, environmental health, and the planet's stored energy. With a significant increase in sequenced fungal genomes, the known diversity of genes encoding organic acids, antibiotics, enzymes, and their pathways has increased exponentially. Currently, over a hundred fungal genome sequences are publicly available; however, no inclusive review has been published. This review is an initiative to address the significance of the fungal genome-sequencing program and provides the road map for basic and applied research.

  20. CATEGORIZATION OF EVENT SEQUENCES FOR LICENSE APPLICATION

    Energy Technology Data Exchange (ETDEWEB)

    G.E. Ragan; P. Mecheret; D. Dexheimer

    2005-04-14

    The purposes of this analysis are: (1) Categorize (as Category 1, Category 2, or Beyond Category 2) internal event sequences that may occur before permanent closure of the repository at Yucca Mountain. (2) Categorize external event sequences that may occur before permanent closure of the repository at Yucca Mountain. This includes examining DBGM-1 seismic classifications and upgrading to DBGM-2, if appropriate, to ensure Beyond Category 2 categorization. (3) State the design and operational requirements that are invoked to make the categorization assignments valid. (4) Indicate the amount of material put at risk by Category 1 and Category 2 event sequences. (5) Estimate frequencies of Category 1 event sequences at the maximum capacity and receipt rate of the repository. (6) Distinguish occurrences associated with normal operations from event sequences. It is beyond the scope of the analysis to propose design requirements that may be required to control radiological exposure associated with normal operations. (7) Provide a convenient compilation of the results of the analysis in tabular form. The results of this analysis are used as inputs to the consequence analyses in an iterative design process that is depicted in Figure 1. Categorization of event sequences for permanent retrieval of waste from the repository is beyond the scope of this analysis. Cleanup activities that take place after an event sequence and other responses to abnormal events are also beyond the scope of the analysis.

  1. Exploration of noncoding sequences in metagenomes.

    Directory of Open Access Journals (Sweden)

    Fabián Tobar-Tosse

    Full Text Available Environment-dependent genomic features have been defined for different metagenomes, whose genes and their associated processes are related to specific environments. Identification of ORFs and their functional categories are the most common methods for association between functional and environmental features. However, this analysis based on finding ORFs misses noncoding sequences and, therefore, some metagenome regulatory or structural information could be discarded. In this work we analyzed 23 whole metagenomes, including coding and noncoding sequences using the following sequence patterns: (G+C content, Codon Usage (Cd, Trinucleotide Usage (Tn, and functional assignments for ORF prediction. Herein, we present evidence of a high proportion of noncoding sequences discarded in common similarity-based methods in metagenomics, and the kind of relevant information present in those. We found a high density of trinucleotide repeat sequences (TRS in noncoding sequences, with a regulatory and adaptive function for metagenome communities. We present associations between trinucleotide values and gene function, where metagenome clustering correlate with microorganism adaptations and kinds of metagenomes. We propose here that noncoding sequences have relevant information to describe metagenomes that could be considered in a whole metagenome analysis in order to improve their organization, classification protocols, and their relation with the environment.

  2. Value of a newly sequenced bacterial genome

    Institute of Scientific and Technical Information of China (English)

    Eudes; GV; Barbosa; Flavia; F; Aburjaile; Rommel; TJ; Ramos; Adriana; R; Carneiro; Yves; Le; Loir; Jan; Baumbach; Anderson; Miyoshi; Artur; Silva; Vasco; Azevedo

    2014-01-01

    Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft(partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.

  3. Revisiting Mendelian disorders through exome sequencing.

    Science.gov (United States)

    Ku, Chee-Seng; Naidoo, Nasheen; Pawitan, Yudi

    2011-04-01

    Over the past several years, more focus has been placed on dissecting the genetic basis of complex diseases and traits through genome-wide association studies. In contrast, Mendelian disorders have received little attention mainly due to the lack of newer and more powerful methods to study these disorders. Linkage studies have previously been the main tool to elucidate the genetics of Mendelian disorders; however, extremely rare disorders or sporadic cases caused by de novo variants are not amendable to this study design. Exome sequencing has now become technically feasible and more cost-effective due to the recent advances in high-throughput sequence capture methods and next-generation sequencing technologies which have offered new opportunities for Mendelian disorder research. Exome sequencing has been swiftly applied to the discovery of new causal variants and candidate genes for a number of Mendelian disorders such as Kabuki syndrome, Miller syndrome and Fowler syndrome. In addition, de novo variants were also identified for sporadic cases, which would have not been possible without exome sequencing. Although exome sequencing has been proven to be a promising approach to study Mendelian disorders, several shortcomings of this method must be noted, such as the inability to capture regulatory or evolutionary conserved sequences in non-coding regions and the incomplete capturing of all exons.

  4. Identification of ancient remains through genomic sequencing

    Science.gov (United States)

    Blow, Matthew J.; Zhang, Tao; Woyke, Tanja; Speller, Camilla F.; Krivoshapkin, Andrei; Yang, Dongya Y.; Derevianko, Anatoly; Rubin, Edward M.

    2008-01-01

    Studies of ancient DNA have been hindered by the preciousness of remains, the small quantities of undamaged DNA accessible, and the limitations associated with conventional PCR amplification. In these studies, we developed and applied a genomewide adapter-mediated emulsion PCR amplification protocol for ancient mammalian samples estimated to be between 45,000 and 69,000 yr old. Using 454 Life Sciences (Roche) and Illumina sequencing (formerly Solexa sequencing) technologies, we examined over 100 megabases of DNA from amplified extracts, revealing unbiased sequence coverage with substantial amounts of nonredundant nuclear sequences from the sample sources and negligible levels of human contamination. We consistently recorded over 500-fold increases, such that nanogram quantities of starting material could be amplified to microgram quantities. Application of our protocol to a 50,000-yr-old uncharacterized bone sample that was unsuccessful in mitochondrial PCR provided sufficient nuclear sequences for comparison with extant mammals and subsequent phylogenetic classification of the remains. The combined use of emulsion PCR amplification and high-throughput sequencing allows for the generation of large quantities of DNA sequence data from ancient remains. Using such techniques, even small amounts of ancient remains with low levels of endogenous DNA preservation may yield substantial quantities of nuclear DNA, enabling novel applications of ancient DNA genomics to the investigation of extinct phyla. PMID:18426903

  5. Enhanced Dynamic Algorithm of Genome Sequence Alignments

    Directory of Open Access Journals (Sweden)

    Arabi E. keshk

    2014-05-01

    Full Text Available The merging of biology and computer science has created a new field called computational biology that explore the capacities of computers to gain knowledge from biological data, bioinformatics. Computational biology is rooted in life sciences as well as computers, information sciences, and technologies. The main problem in computational biology is sequence alignment that is a way of arranging the sequences of DNA, RNA or protein to identify the region of similarity and relationship between sequences. This paper introduces an enhancement of dynamic algorithm of genome sequence alignment, which called EDAGSA. It is filling the three main diagonals without filling the entire matrix by the unused data. It gets the optimal solution with decreasing the execution time and therefore the performance is increased. To illustrate the effectiveness of optimizing the performance of the proposed algorithm, it is compared with the traditional methods such as Needleman-Wunsch, Smith-Waterman and longest common subsequence algorithms. Also, database is implemented for using the algorithm in multi-sequence alignments for searching the optimal sequence that matches the given sequence.

  6. Large Zero Autocorrelation Zone of Golay Sequences and $4^q$-QAM Golay Complementary Sequences

    CERN Document Server

    Gong, Guang; Yang, Yang

    2011-01-01

    Sequences with good correlation properties have been widely adopted in modern communications, radar and sonar applications. In this paper, we present our new findings on some constructions of single $H$-ary Golay sequence and $4^q$-QAM Golay complementary sequence with a large zero autocorrelation zone, where $H\\ge 2$ is an arbitrary even integer and $q\\ge 2$ is an arbitrary integer. Those new results on Golay sequences and QAM Golay complementary sequences can be explored during synchronization and detection at the receiver end and thus improve the performance of the communication system.

  7. Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences

    DEFF Research Database (Denmark)

    Karlskov-Mortensen, Peter; Hu, Z.L.; Gorodkin, Jan

    2007-01-01

    the human genome (BLAST cut-off threshold = 1 x 10-5). All microsatellite sequences placed on the comparative map are accessible at http://www.animalgenome.org/QTLdb/pig.html . These sequences increase the number of identified microsatellites in the porcine genome by several orders of magnitude......A total of 10 882 porcine microsatelite repeats were identified in genomic shotgun sequences from the Sino-Danish Pig Genome Sequencing Consortium ( http://piggenome.dk ). Of these, 4528 microsatellites were placed on a pig-human comparative map by BLAST analysis of porcine sequences against...

  8. Robot Sequencing and Visualization Program (RSVP)

    Science.gov (United States)

    Cooper, Brian K.; Maxwell,Scott A.; Hartman, Frank R.; Wright, John R.; Yen, Jeng; Toole, Nicholas T.; Gorjian, Zareh; Morrison, Jack C

    2013-01-01

    The Robot Sequencing and Visualization Program (RSVP) is being used in the Mars Science Laboratory (MSL) mission for downlink data visualization and command sequence generation. RSVP reads and writes downlink data products from the operations data server (ODS) and writes uplink data products to the ODS. The primary users of RSVP are members of the Rover Planner team (part of the Integrated Planning and Execution Team (IPE)), who use it to perform traversability/articulation analyses, take activity plan input from the Science and Mission Planning teams, and create a set of rover sequences to be sent to the rover every sol. The primary inputs to RSVP are downlink data products and activity plans in the ODS database. The primary outputs are command sequences to be placed in the ODS for further processing prior to uplink to each rover. RSVP is composed of two main subsystems. The first, called the Robot Sequence Editor (RoSE), understands the MSL activity and command dictionaries and takes care of converting incoming activity level inputs into command sequences. The Rover Planners use the RoSE component of RSVP to put together command sequences and to view and manage command level resources like time, power, temperature, etc. (via a transparent realtime connection to SEQGEN). The second component of RSVP is called HyperDrive, a set of high-fidelity computer graphics displays of the Martian surface in 3D and in stereo. The Rover Planners can explore the environment around the rover, create commands related to motion of all kinds, and see the simulated result of those commands via its underlying tight coupling with flight navigation, motor, and arm software. This software is the evolutionary replacement for the Rover Sequencing and Visualization software used to create command sequences (and visualize the Martian surface) for the Mars Exploration Rover mission.

  9. Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

    Directory of Open Access Journals (Sweden)

    Jian eWu

    2012-11-01

    Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

  10. Effects of the Ion PGM™ Hi-Q™ sequencing chemistry on sequence data quality.

    Science.gov (United States)

    Churchill, Jennifer D; King, Jonathan L; Chakraborty, Ranajit; Budowle, Bruce

    2016-09-01

    Massively parallel sequencing (MPS) offers substantial improvements over current forensic DNA typing methodologies such as increased resolution, scalability, and throughput. The Ion PGM™ is a promising MPS platform for analysis of forensic biological evidence. The system employs a sequencing-by-synthesis chemistry on a semiconductor chip that measures a pH change due to the release of hydrogen ions as nucleotides are incorporated into the growing DNA strands. However, implementation of MPS into forensic laboratories requires a robust chemistry. Ion Torrent's Hi-Q™ Sequencing Chemistry was evaluated to determine if it could improve on the quality of the generated sequence data in association with selected genetic marker targets. The whole mitochondrial genome and the HID-Ion STR 10-plex panel were sequenced on the Ion PGM™ system with the Ion PGM™ Sequencing 400 Kit and the Ion PGM™ Hi-Q™ Sequencing Kit. Concordance, coverage, strand balance, noise, and deletion ratios were assessed in evaluating the performance of the Ion PGM™ Hi-Q™ Sequencing Kit. The results indicate that reliable, accurate data are generated and that sequencing through homopolymeric regions can be improved with the use of Ion Torrent's Hi-Q™ Sequencing Chemistry. Overall, the quality of the generated sequencing data supports the potential for use of the Ion PGM™ in forensic genetic laboratories.

  11. Statistical properties of filtered pseudorandom digital sequences formed from the sum of maximum-length sequences

    Science.gov (United States)

    Wallace, G. R.; Weathers, G. D.; Graf, E. R.

    1973-01-01

    The statistics of filtered pseudorandom digital sequences called hybrid-sum sequences, formed from the modulo-two sum of several maximum-length sequences, are analyzed. The results indicate that a relation exists between the statistics of the filtered sequence and the characteristic polynomials of the component maximum length sequences. An analysis procedure is developed for identifying a large group of sequences with good statistical properties for applications requiring the generation of analog pseudorandom noise. By use of the analysis approach, the filtering process is approximated by the convolution of the sequence with a sum of unit step functions. A parameter reflecting the overall statistical properties of filtered pseudorandom sequences is derived. This parameter is called the statistical quality factor. A computer algorithm to calculate the statistical quality factor for the filtered sequences is presented, and the results for two examples of sequence combinations are included. The analysis reveals that the statistics of the signals generated with the hybrid-sum generator are potentially superior to the statistics of signals generated with maximum-length generators. Furthermore, fewer calculations are required to evaluate the statistics of a large group of hybrid-sum generators than are required to evaluate the statistics of the same size group of approximately equivalent maximum-length sequences.

  12. How Long is an Aftershock Sequence?

    Science.gov (United States)

    Godano, Cataldo; Tramelli, Anna

    2016-07-01

    The occurrence of a mainschok is always followed by aftershocks spatially distributed within the fault area. The aftershocks rate decay with time is described by the empirical Omori law which was inferred by catalogues analysis. The sequences discrimination within catalogues is not a straightforward operation, especially for low-magnitude mainshocks. Here, we describe the rate decay of the Omori law obtained using different sequence discrimination tools and we discover that, when the background seismicity is excluded, the sequences tend to last for the temporal extension of the catalogue.

  13. Nanopore-CMOS Interfaces for DNA Sequencing.

    Science.gov (United States)

    Magierowski, Sebastian; Huang, Yiyun; Wang, Chengjie; Ghafar-Zadeh, Ebrahim

    2016-08-06

    DNA sequencers based on nanopore sensors present an opportunity for a significant break from the template-based incumbents of the last forty years. Key advantages ushered by nanopore technology include a simplified chemistry and the ability to interface to CMOS technology. The latter opportunity offers substantial promise for improvement in sequencing speed, size and cost. This paper reviews existing and emerging means of interfacing nanopores to CMOS technology with an emphasis on massively-arrayed structures. It presents this in the context of incumbent DNA sequencing techniques, reviews and quantifies nanopore characteristics and models and presents CMOS circuit methods for the amplification of low-current nanopore signals in such interfaces.

  14. Initial retrieval sequence and blending strategy

    Energy Technology Data Exchange (ETDEWEB)

    Pemwell, D.L.; Grenard, C.E.

    1996-09-01

    This report documents the initial retrieval sequence and the methodology used to select it. Waste retrieval, storage, pretreatment and vitrification were modeled for candidate single-shell tank retrieval sequences. Performance of the sequences was measured by a set of metrics (for example,high-level waste glass volume, relative risk and schedule).Computer models were used to evaluate estimated glass volumes,process rates, retrieval dates, and blending strategy effects.The models were based on estimates of component inventories and concentrations, sludge wash factors and timing, retrieval annex limitations, etc.

  15. The double main sequence of Omega Centauri

    CERN Document Server

    Bedin, L R

    2004-01-01

    Recent, high precision photometry of Omega Centauri, the biggest Galactic globular cluster, has been obtained with Hubble Space Telescope. The color magnitude diagram reveals an unexpected bifurcation of colors in the main sequence (MS). The newly found double MS, the multiple turnoffs and subgiant branches, and other sequences discovered in the past along the red giant branch of this cluster add up to a fascinating but frustrating puzzle. Among the possible explanations for the blue main sequence an anomalous overabundance of helium is suggested. The hypothesis will be tested with a set of FLAMES@VLT data we have recently obtained (ESO DDT program), and with forthcoming ACS@HST images.

  16. Association Claims in the Sequencing Era

    Directory of Open Access Journals (Sweden)

    Sara L. Pulit

    2014-03-01

    Full Text Available Since the completion of the Human Genome Project, the field of human genetics has been in great flux, largely due to technological advances in studying DNA sequence variation. Although community-wide adoption of statistical standards was key to the success of genome-wide association studies, similar standards have not yet been globally applied to the processing and interpretation of sequencing data. It has proven particularly challenging to pinpoint unequivocally disease variants in sequencing studies of polygenic traits. Here, we comment on a number of factors that may contribute to irreproducible claims of association in scientific literature and discuss possible steps that we can take towards cultural change.

  17. Persistence and NIP in the characteristic sequence

    CERN Document Server

    Malliaris, M E

    2009-01-01

    For a first-order formula $\\phi(x;y)$ we introduce and study the characteristic sequence $$ of hypergraphs defined by $P_n(y_1,...,y_n) := (\\exists x) \\bigwedge_{i \\leq n} \\phi(x;y_i)$. We show that combinatorial and classification theoretic properties of the characteristic sequence reflect classification theoretic properties of $\\varphi$ and vice versa. Specifically, we show that some tree properties are detected by the presence of certain combinatorial configurations in the characteristic sequence while other properties such as instability and the independence property manifest themselves in the persistence of complicated configurations under localization.

  18. Scale-PC shielding analysis sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bowman, S.M.

    1996-05-01

    The SCALE computational system is a modular code system for analyses of nuclear fuel facility and package designs. With the release of SCALE-PC Version 4.3, the radiation shielding analysis community now has the capability to execute the SCALE shielding analysis sequences contained in the control modules SAS1, SAS2, SAS3, and SAS4 on a MS- DOS personal computer (PC). In addition, SCALE-PC includes two new sequences, QADS and ORIGEN-ARP. The capabilities of each sequence are presented, along with example applications.

  19. Spreadsheet macros for coloring sequence alignments.

    Science.gov (United States)

    Haygood, M G

    1993-12-01

    This article describes a set of Microsoft Excel macros designed to color amino acid and nucleotide sequence alignments for review and preparation of visual aids. The colored alignments can then be modified to emphasize features of interest. Procedures for importing and coloring sequences are described. The macro file adds a new menu to the menu bar containing sequence-related commands to enable users unfamiliar with Excel to use the macros more readily. The macros were designed for use with Macintosh computers but will also run with the DOS version of Excel.

  20. Microbial genomics: from sequence to function.

    OpenAIRE

    Schwartz, I

    2000-01-01

    The era of genomics (the study of genes and their function) began a scant dozen years ago with a suggestion by James Watson that the complete DNA sequence of the human genome be determined. Since that time, the human genome project has attracted a great deal of attention in the scientific world and the general media; the scope of the sequencing effort, and the extraordinary value that it will provide, has served to mask the enormous progress in sequencing other genomes. Microbial genome seque...